### Start ref-cache Server

Source: https://www.htslib.org/doc/ref-cache.html

Create directories for cache and logs, then start the ref-cache server in the background listening on port 8080 with a specified upstream source.

```bash
mkdir cached_refs
mkdir logs
ref-cache -b -d cached_refs -l logs -p 8080 -u https://www.ebi.ac.uk/ena/cram/md5/
```

--------------------------------

### Example Samtools Checksum Output

Source: https://www.htslib.org/doc/samtools-checksum.html

This example shows the typical output format for samtools checksums, including header information and the checksum table for different read groups and QC statuses.

```text
# Checksum for file: NA12892.chrom20.ILLUMINA.bwa.CEU.high_coverage.bam
# Aux tags:          BC,FI,QT,RT,TC
# BAM flags:         PAIRED,READ1,READ2


# Group    QC        count  flag+seq  +name     +qual     +aux      combined
all        all    42890086  71169bbb  633fd9f7  2a2e693f  71169bbb  09d03ed4
SRR010946  all      262249  2957df86  3b6dcbc9  66be71f7  2957df86  58e89c25
SRR002165  all       97846  47ff17e0  6ff8fc7b  58366bf5  47ff17e0  796eecb0
[...cut...]

```

--------------------------------

### HAP/SAMPLE to VCF Conversion Examples

Source: https://www.htslib.org/doc/bcftools.html

Demonstrates the format of .hap files when using the --vcf-ids option and the default format for the --hapsample2vcf command.

```text
  .hap (with --vcf-ids)
  ---------------------
  1:111485207_G_A rsID1 111485207 G A 0 1 0 0
  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0

  .hap (the default)
  ------------------
  1 1:111485207_G_A 111485207 G A 0 1 0 0
  1 1:111495231_A_<DEL>_111495784 111495231 A <DEL> 0 0 1 0
```

--------------------------------

### Bcftools String Comparison Examples

Source: https://www.htslib.org/doc/bcftools.html

Demonstrates case-insensitive string comparisons and OR logic for comma-separated values.

```bash
-i 'TAG="hello,world"'
-i 'TAG="hello" || TAG="world"'
-i 'TAG="hello" && TAG="world"'
```

--------------------------------

### INFO and FORMAT Tags

Source: https://www.htslib.org/doc/bcftools.html

Examples of how to reference INFO and FORMAT tags, including common column names.

```plaintext
INFO/DP or DP
FORMAT/DV, FMT/DV, or DV
FILTER, QUAL, ID, CHROM, POS, REF, ALT[0]
```

--------------------------------

### samtools flagstat default output example

Source: https://www.htslib.org/doc/samtools-flagstat.html

Example of the default output format for samtools flagstat, showing total reads and specific categories with percentages.

```text
122 + 28 in total (QC-passed reads + QC-failed reads)
32 + 0 mapped (94.12% : N/A)
```

--------------------------------

### Bcftools Vector Query Examples

Source: https://www.htslib.org/doc/bcftools.html

Illustrates querying multiple values in a vector using OR logic and specific index access.

```bash
-i 'TAG[*]=1'   .. true, the record will be printed
-i 'TAG[*]!=1'  .. true
-e 'TAG[*]=1'   .. false, the record will be discarded
-e 'TAG[*]!=1'  .. false
-i 'TAG[0]=1'   .. true
-i 'TAG[0]!=1'  .. false
-e 'TAG[0]=1'   .. false
-e 'TAG[0]!=1'  .. true
```

--------------------------------

### Compress and Index a GFF File

Source: https://www.htslib.org/doc/1.2.1/tabix.html

This example demonstrates how to compress a GFF file using bgzip and then index it with tabix for efficient querying. It first filters and sorts the GFF content before compression.

```bash
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;

```

```bash
tabix -p gff sorted.gff.gz;

```

--------------------------------

### HAP/LEGEND/SAMPLE Conversion Examples

Source: https://www.htslib.org/doc/bcftools.html

Shows the expected format for .hap, .legend, and .sample files when converting to/from VCF using IMPUTE2/SHAPEIT formats.

```text
  .hap
  -----
  0 1 0 0 1 0
  0 1 0 0 0 1

  .legend
  -------
  id position a0 a1
  1:111485207_G_A 111485207 G A
  1:111494194_C_T 111494194 C T

  .sample
  -------
  sample population group sex
  sample1 sample1 sample1 2
  sample2 sample2 sample2 2
```

--------------------------------

### Split and Checksum BAM Files

Source: https://www.htslib.org/doc/samtools-checksum.html

This example demonstrates how to split a BAM file, compute checksums for the original and split files, and then compare them to verify data integrity. It uses shell commands to manage the process.

```bash
samtools split -u /tmp/split/noRG.bam -f '/tmp/split/%!.%.' in.cram
samtools checksum -a in.cram -o in.chksum
s=$(for i in /tmp/split/*.bam;do echo "<("samtools checksum -a $i")";done)
eval samtools checksum -m $s -o split.chksum
diff in.chksum split.chksum
```

--------------------------------

### Get Plugin Usage Information

Source: https://www.htslib.org/doc/bcftools.html

Displays detailed usage information for a specific plugin, such as 'dosage'.

```bash
bcftools +dosage -h
```

--------------------------------

### Sex Column Format Example

Source: https://www.htslib.org/doc/bcftools.html

Illustrates the required format for the sex file used with the --sex option.

```text
    MaleSample    M
    FemaleSample  F
```

--------------------------------

### Example Primer BED File Format

Source: https://www.htslib.org/doc/samtools-ampliconstats.html

Specifies primer locations for amplicons. Each line defines a region with LEFT and RIGHT primers.

```bed
MN908947.3  1875  1897  nCoV-2019_7_LEFT        60  +
MN908947.3  1868  1890  nCoV-2019_7_LEFT_alt0   60  +
MN908947.3  2247  2269  nCoV-2019_7_RIGHT       60  -
MN908947.3  2242  2264  nCoV-2019_7_RIGHT_alt5  60  -
MN908947.3  2181  2205  nCoV-2019_8_LEFT        60  +
MN908947.3  2568  2592  nCoV-2019_8_RIGHT       60  -
```

--------------------------------

### Minimal GFF3 example for bcftools csq

Source: https://www.htslib.org/doc/bcftools.html

This example demonstrates the minimal structure required for a GFF3 file to be used with bcftools csq. It includes gene, transcript, UTR, and CDS features with necessary attributes.

```plaintext
# The program looks for "CDS", "exon", "three_prime_UTR" and "five_prime_UTR" lines,
# looks up their parent transcript (determined from the "Parent=transcript:" attribute),
# the gene (determined from the transcript's "Parent=gene:" attribute), and the biotype
# (the most interesting is "protein_coding").
#
# Empty and commented lines are skipped, the following GFF columns are required
#   1.  chromosome
#   2.  IGNORED
#   3.  type (CDS, exon, three_prime_UTR, five_prime_UTR, gene, transcript, etc.)
#   4.  start of the feature (1-based)
#   5.  end of the feature (1-based)
#   6.  IGNORED
#   7.  strand (+ or -)
#   8.  phase (0, 1, 2 or .)
#   9.  semicolon-separated attributes (see below)
#
# Attributes required for
#   gene lines:
#   - ID=gene:<gene_id>
#   - biotype=<biotype>
#   - Name=<gene_name>      [optional]
#
#   transcript lines:
#   - ID=transcript:<transcript_id>
#   - Parent=gene:<gene_id>
#   - biotype=<biotype>
#
#   other lines (CDS, exon, five_prime_UTR, three_prime_UTR):
#   - Parent=transcript:<transcript_id>
#
# Supported biotypes:
#   - see the function gff_parse_biotype() in bcftools/csq.c

1   ignored_field  gene            21  2148  .   -   .   ID=gene:GeneId;biotype=protein_coding;Name=GeneName
1   ignored_field  transcript      21  2148  .   -   .   ID=transcript:TranscriptId;Parent=gene:GeneId;biotype=protein_coding
1   ignored_field  three_prime_UTR 21  2054  .   -   .   Parent=transcript:TranscriptId
1   ignored_field  exon            21  2148  .   -   .   Parent=transcript:TranscriptId
1   ignored_field  CDS             21  2148  .   -   1   Parent=transcript:TranscriptId
1   ignored_field  five_prime_UTR  210 2148  .   -   .   Parent=transcript:TranscriptId

```

--------------------------------

### TSV to VCF Conversion Example 2

Source: https://www.htslib.org/doc/bcftools.html

Converts a tab-delimited file into a sites-only VCF, ignoring the first column and specifying REF and ALT alleles.

```bash
bcftools convert -c -,CHROM,POS,REF,ALT -f ref.fa --tsv2vcf calls.txt -o out.bcf
```

--------------------------------

### Specify Allowed Client Networks

Source: https://www.htslib.org/doc/ref-cache.html

Use the -m option to define the allowed client networks for the ref-cache server. This example allows connections from a specific CIDR block and the default private ranges.

```bash
ref-cache -m 192.0.2.0/24 -m default ...
```

--------------------------------

### Define Header Lines for Annotations

Source: https://www.htslib.org/doc/bcftools.html

Provides examples of custom header lines for INFO tags, specifying their ID, Number, Type, and Description.

```vcf
##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
```

--------------------------------

### Sample Annotation File Format

Source: https://www.htslib.org/doc/bcftools.html

This is an example of a tab-delimited annotation file. It includes columns for CHROM, POS, a string tag, and a numeric tag. Ensure your annotation file matches the expected format for bcftools annotate.

```text
# Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
1  752566  SomeString      5
1  798959  SomeOtherString 6
```

--------------------------------

### Set output format for pipeline usage

Source: https://www.htslib.org/doc/samtools-reset.html

Demonstrates setting the output format to BAM with compression level 0 for use in a pipeline. This example chains samtools collate, samtools reset, and a hypothetical aligner.

```bash
samtools collate -O -u input.cram |
  samtools reset --output-fmt BAM,level=0 |
  myaligner -I bam -o out.bam
```

--------------------------------

### Annotate TSV with Header Mapping and Special Annotations

Source: https://www.htslib.org/doc/annot-tsv.html

This example demonstrates transferring fields and adding special annotations ('nbp', 'cnt') by mapping columns using header names from the target file. The output includes original fields and new annotations.

```bash
annot-tsv -s src.txt.gz -t tgt_hdr.txt.gz -c chr,beg,end:chrom,from,to -m sample -f type,qual -a nbp,cnt:pair,count
```

--------------------------------

### Specify Sample List

Source: https://www.htslib.org/doc/bcftools.html

Provide a list of sample names to include or exclude. Refer to 'Common Options' for details.

```bash
-s, --samples LIST
    
    list of sample names. See **Common Options**
```

--------------------------------

### Run a Plugin

Source: https://www.htslib.org/doc/bcftools.html

Executes a specified plugin with an input VCF file.

```bash
bcftools plugin counts in.vcf
```

--------------------------------

### BCSQ Annotation Example: Stop Gained Variant

Source: https://www.htslib.org/doc/bcftools.html

Provides an example of BCSQ annotation for a stop gained variant, specifying the consequence type, gene name, transcript ID, and the specific variant causing the stop gain.

```plaintext
BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T
```

--------------------------------

### List Available Plugins

Source: https://www.htslib.org/doc/bcftools.html

Lists all plugins that are currently available for use with bcftools.

```bash
bcftools plugin -l
```

--------------------------------

### Annotate Output with FORMAT/INFO Tags

Source: https://www.htslib.org/doc/bcftools.html

Specify FORMAT and INFO tags to include in the output. Use '?' to list available tags.

```bash
-a, --annotate LIST
    
    Comma-separated list of FORMAT and INFO tags to output. (case-insensitive, the "FORMAT/" prefix is optional, and use "?" to list available annotations on the command line) [null]:
```
FORMAT/AD   .. Allelic depth (Number=R,Type=Integer)
FORMAT/ADF  .. Allelic depths on the forward strand (Number=R,Type=Integer)
FORMAT/ADR  .. Allelic depths on the reverse strand (Number=R,Type=Integer)
FORMAT/DP   .. Number of high-quality bases (Number=1,Type=Integer)
FORMAT/SP   .. Phred-scaled strand bias P-value (Number=1,Type=Integer)
FORMAT/SCR  .. Number of soft-clipped reads (Number=1,Type=Integer)

INFO/AD     .. Total allelic depth (Number=R,Type=Integer)
INFO/ADF    .. Total allelic depths on the forward strand (Number=R,Type=Integer)
INFO/ADR    .. Total allelic depths on the reverse strand (Number=R,Type=Integer)
INFO/SCR    .. Number of soft-clipped reads (Number=1,Type=Integer)

FORMAT/DV   .. Deprecated in favor of FORMAT/AD; Number of high-quality non-reference bases, (Number=1,Type=Integer)
FORMAT/DP4  .. Deprecated in favor of FORMAT/ADF and FORMAT/ADR; Number of high-quality ref-forward, ref-reverse,
               alt-forward and alt-reverse bases (Number=4,Type=Integer)
FORMAT/DPR  .. Deprecated in favor of FORMAT/AD; Number of high-quality bases for each observed allele (Number=R,Type=Integer)
INFO/DPR    .. Deprecated in favor of INFO/AD; Number of high-quality bases for each observed allele (Number=R,Type=Integer)
```
```

--------------------------------

### Prepopulating Reference Cache with FASTA Files

Source: https://www.htslib.org/doc/reference_seqs.html

Use the seq_cache_populate.pl script to pre-populate a local reference cache from FASTA files. This is useful for cloud environments to ensure local network access.

```bash
seq_cache_populate.pl -root=/local/refs -subdirs 2 *.fa

```

--------------------------------

### BCFtools Filter Expression

Source: https://www.htslib.org/doc/bcftools.html

Example of filtering VCF records using an expression with BCFtools. Expressions should be quoted to prevent shell interpretation.

```shell
bcftools view -i 'ID!="." & MAF[0]<0.01'
```

--------------------------------

### Samtools mpileup to Show All Alignments

Source: https://www.htslib.org/doc/samtools-mpileup.html

Use options like --count-orphans, --no-BAQ, --max-depth 0, --min-BQ 0, --excl-flags 0, and --disable-overlap-removal to display all possible alignments without filtering or modification.

```bash
samtools mpileup --count-orphans --no-BAQ --max-depth 0 --fasta-ref ref_file.fa \
--min-BQ 0 --excl-flags 0 --disable-overlap-removal in.sam
```

```bash
samtools mpileup -A -B -d 0 -f ref_file.fa -Q 0 --ff 0 -x in.sam
```

--------------------------------

### Sample Filtering with File

Source: https://www.htslib.org/doc/bcftools.html

Demonstrates filtering based on sample names provided in an external file.

```plaintext
GT[@samples.txt]="het" & binom(AD)<0.01
```

--------------------------------

### Get CRAM File Size Information

Source: https://www.htslib.org/doc/samtools.html

Retrieves verbose size information for a CRAM file. Useful for understanding compression efficiency.

```bash
samtools cram-size -v -o out.size in.cram
```

--------------------------------

### Remove comment lines from header

Source: https://www.htslib.org/doc/samtools-reheader.html

Use the `-c` option with `grep` to filter out lines starting with `@CO` from the header. This is useful for cleaning up header information.

```bash
samtools reheader -c 'grep -v ^@CO' in.bam
```

--------------------------------

### BCSQ Annotation Example: Downstream Stop Variant

Source: https://www.htslib.org/doc/bcftools.html

Demonstrates the BCSQ annotation for a variant downstream from a stop codon, where the consequence type is prefixed with an asterisk (*).

```plaintext
BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C
```

--------------------------------

### List Common Plugin Options

Source: https://www.htslib.org/doc/bcftools.html

Lists options that are common to all bcftools plugins.

```bash
bcftools plugin
```

--------------------------------

### Specify Sample File

Source: https://www.htslib.org/doc/bcftools.html

Use a file containing sample names for inclusion or exclusion (prefix with '^'). This file can also be used for renaming samples.

```bash
-S, --samples-file FILE
    
    file of sample names to include or exclude if prefixed with "^". One sample per line. This file can also be used to rename samples by giving the new sample name as a second white-space-separated column, like this: "old_name new_name". If a sample name contains spaces, the spaces can be escaped using the backslash character, for example "Not\ a\ good\ sample\ name".
```

--------------------------------

### Samtools mpileup with Range Specification

Source: https://www.htslib.org/doc/samtools-mpileup.html

Use the -r option to specify a region for processing. Index files can be implicit or explicit.

```bash
samtools mpileup in1.bam in2.sam.gz -r chr10:100000-200000
```

```bash
samtools mpileup in1.bam in2.sam.gz idx/in1.csi idx/in2.csi -X -r chr10:100000-200000
```

```bash
samtools mpileup -b fofn -r chr10:100000-200000
```

--------------------------------

### TSV to VCF Conversion Example 1

Source: https://www.htslib.org/doc/bcftools.html

Converts 23andme results into VCF format, specifying column order, sample name, and reference FASTA file.

```bash
bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -o out.vcf.gz
```

--------------------------------

### Create and Index a GFF File with Tabix

Source: https://www.htslib.org/doc/tabix.html

This snippet demonstrates how to sort, compress, and index a GFF file using standard Unix tools and tabix. It first filters and sorts the GFF file, then compresses it with bgzip, and finally creates a tabix index.

```bash
(grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\t'`" -k1,1 -k4,4n) | bgzip > sorted.gff.gz; 
tabix -p gff sorted.gff.gz
```

--------------------------------

### Index Allele Frequency File with Tabix

Source: https://www.htslib.org/doc/bcftools.html

Indexes the prepared allele frequency file (AFs.tab.gz) for efficient lookup by bcftools annotate. Requires tabix to be installed.

```bash
tabix -s1 -b2 -e2 AFs.tab.gz
```

--------------------------------

### Sample-level Functions in Bcftools

Source: https://www.htslib.org/doc/bcftools.html

Use SMPL_ prefixed functions to evaluate per-sample values on FORMAT tags for site selection.

```bash
SMPL_MAX, SMPL_MIN, SMPL_AVG, SMPL_MEAN, SMPL_MEDIAN, SMPL_STDEV, SMPL_SUM, SMPL_COUNT,
sMAX, sMIN, sAVG, sMEAN, sMEDIAN, sSTDEV, sSUM, sCOUNT
```

--------------------------------

### Indexing a BGZF-compressed file with tabix

Source: https://www.htslib.org/doc/bcftools.html

This command indexes a BGZF-compressed file for use with tabix. It specifies the chromosome column, start position column, and end position column.

```bash
tabix -s1 -b2 -e3 file.gz
```

--------------------------------

### Basic bcftools csq Usage

Source: https://www.htslib.org/doc/bcftools.html

This snippet shows the basic command structure for running bcftools csq, specifying the reference FASTA, GFF annotation file, input VCF, and output BCF file.

```bash
bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf
```

--------------------------------

### BCSQ Annotation Example: Frameshift Insertion

Source: https://www.htslib.org/doc/bcftools.html

Shows the BCSQ annotation for an inframe insertion, resulting from a frame-restoring combination of two frameshift insertions. It includes the position of the full annotation.

```plaintext
BCSQ=@46115084
BCSQ=inframe_insertion|COPZ2|ENST00000006101|-|18AGRGP>18AQAGGP|46115072C>CG+46115084T>TGG
```

--------------------------------

### Run a Plugin with Abbreviated Notation

Source: https://www.htslib.org/doc/bcftools.html

Runs a plugin using the shorthand '+' notation, which is equivalent to the full 'plugin' command.

```bash
bcftools +counts in.vcf
```

--------------------------------

### Print Samples with Custom BAI Index Files

Source: https://www.htslib.org/doc/samtools-samples.html

Uses custom .bai index files to determine the indexing status of BAM files. This is helpful when index files are named differently or located separately.

```bash
$ samtools samples -i -h -X S1.bam S2.bam S1.bam.bai S2.bam.bai
#SM	PATH	INDEX
S1	S1.bam	Y
S2	S2.bam	Y
```

--------------------------------

### Atomize Variants with '.' Overlap

Source: https://www.htslib.org/doc/bcftools.html

This example shows how to decompose complex variants into simpler ones using bcftools norm with the --atomize option and setting overlapping variants to missing ('.').

```bash
bcftools norm -a --atom-overlaps . file.vcf.gz
```

--------------------------------

### Include customized index file location

Source: https://www.htslib.org/doc/samtools-merge.html

This example shows how to specify custom locations for index files when merging BAM files, particularly when the index files are not in the default data folder.

```bash
samtools merge [options] -X <out.bam> </data_folder/in1.bam> [</data_folder/in2.bam> ... </data_folder/inN.bam>] </index_folder/index1.bai> [</index_folder/index2.bai> ... </index_folder/indexN.bai>]
```

--------------------------------

### Print Samples with Header

Source: https://www.htslib.org/doc/samtools-samples.html

Extracts sample names from BAM/SAM files and includes a header. Useful when sample names are present in the @RG line.

```bash
$ samtools  samples -h S*.bam *.sam
#SM	PATH
S1	S1.bam
S2	S2.bam
S3	S3.bam
S4	S4.bam
S5	S5.bam
.	example.sam
```

--------------------------------

### Text Alignment Viewer

Source: https://www.htslib.org/doc/samtools.html

Launches a text-based alignment viewer using the ncurses library. Press '?' for help and 'g' to jump to a region.

```bash
samtools tview ["-p" _chr:pos_] ["-s" _STR_] ["-d" _display_] <in.sorted.bam> [ref.fasta]
```

--------------------------------

### Create BED File Format

Source: https://www.htslib.org/doc/bcftools.html

Generates a BED file format (chromosome, 0-based start position, 1-based end position, and ID) from VCF/BCF data. This is useful for genomic interval representation.

```bash
# Make a BED file: chr, pos (0-based), end pos (1-based), id
bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf
```

--------------------------------

### Filter Samples by FORMAT/DP Value (OR Operator)

Source: https://www.htslib.org/doc/bcftools.html

Prints sample, genotype, and DP for all samples at sites where at least one sample has DP equal to 1 or 2. This example uses the logical OR operator `||`.

```bash
# Print all samples at sites where at least one sample has DP=1 or DP=2. In the second case
# print only samples with DP=1 or DP=2, the difference is in the logical operator used, || vs |.
bcftools query -f '[%SAMPLE %GT %DP\n]' -i 'FMT/DP=1 || FMT/DP=2' file.vcf
```

--------------------------------

### Atomize Variants with Escaped '*' Overlap

Source: https://www.htslib.org/doc/bcftools.html

This example shows decomposing complex variants using bcftools norm with --atomize and setting overlapping variants to the star allele ('*'), using shell escaping for the asterisk.

```bash
bcftools norm -a --atom-overlaps \* file.vcf.gz
```

--------------------------------

### Atomize Variants with '*' Overlap

Source: https://www.htslib.org/doc/bcftools.html

This example demonstrates decomposing complex variants using bcftools norm with --atomize and setting overlapping variants to the star allele ('*'). Note the need to quote or escape the asterisk.

```bash
bcftools norm -a --atom-overlaps '*' file.vcf.gz
```

--------------------------------

### Display Beginning of BAM File

Source: https://www.htslib.org/doc/samtools.html

Displays the first few records of a BAM file. Useful for a quick inspection of file content.

```bash
samtools head in.bam
```

--------------------------------

### Navigate to a specific position with samtools tview

Source: https://www.htslib.org/doc/samtools-tview.html

Use the -p option to specify an initial position for the alignment viewer. The position can be in 'chr:pos' format.

```bash
samtools tview -p 1:234567 in.bam
```

--------------------------------

### Filter Samples by FORMAT/DP Value (Single Pipe Operator)

Source: https://www.htslib.org/doc/bcftools.html

Prints sample, genotype, and DP for all samples at sites where at least one sample has DP equal to 1 or 2. This example uses the logical OR operator `|`.

```bash
bcftools query -f '[%SAMPLE %GT %DP\n]' -i 'FMT/DP=1 |  FMT/DP=2' file.vcf
```

--------------------------------

### Index FASTQ File

Source: https://www.htslib.org/doc/samtools.html

Creates an index for a FASTQ file. This allows for faster random access to sequences within the FASTQ file.

```bash
samtools fqidx ref.fastq
```

--------------------------------

### Filter indel clusters with bcftools

Source: https://www.htslib.org/doc/bcftools.html

Use --IndelGap to filter clusters of indels separated by a specified number of base pairs, allowing only one to pass. The example demonstrates the filtering logic for indel clusters.

```bash
bcftools filter --IndelGap 2 file.vcf
```

--------------------------------

### Create Sequence Dictionary

Source: https://www.htslib.org/doc/samtools.html

Creates a sequence dictionary (a FASTA index file) for a reference FASTA file. Requires reference name and assembly attributes.

```bash
samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta
```

--------------------------------

### Discard PG entries from a specific ID onwards

Source: https://www.htslib.org/doc/samtools-reset.html

Removes Program Group (PG) lines from the header starting with the specified ID ('bwa_index') and all subsequent PG lines. Use this to clean up header information from specific aligners.

```bash
samtools reset -o out.sam --reject-PG=bwa_index
```