Samtools

https://www.htslib.org/doc/samtools.html
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Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM,...
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### samtools samples: List read groups and samples

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

Lists the read groups and samples present in the input BAM file.

```bash
samtools samples input.bam
```

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

### samtools import: Convert FASTQ to BAM

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

Converts a FASTQ file to BAM format and writes to standard output.

```bash
samtools import input.fastq > output.bam
```

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

### samtools phase: Phase BAM file

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

Phases the input BAM file.

```bash
samtools phase input.bam
```

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

### samtools dict: Create sequence dictionary

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

Creates a sequence dictionary file for the reference FASTA. The -a option specifies the assembly name and -s the species.

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

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

### samtools fastq: Convert BAM to FASTQ

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

Converts the input BAM file to FASTQ format and writes to standard output.

```bash
samtools fastq input.bam > output.fastq
```

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

### samtools head: Print BAM header

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

Prints the header of the input BAM file.

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

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

### samtools fqidx: Index FASTQ file

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

Indexes a FASTQ file for random access.

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

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

### samtools index: Index BAM file

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

Creates an index for the sorted BAM file.

```bash
samtools index aln.sorted.bam
```

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

### samtools faidx: Index FASTA file

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

Indexes the reference FASTA file for fast random access.

```bash
samtools faidx ref.fasta
```

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

### samtools coverage: Report coverage statistics

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

Reports coverage statistics for the sorted BAM file.

```bash
samtools coverage aln.sorted.bam
```

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

### samtools tview: Interactive alignment viewer

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

Displays an interactive text-based alignment viewer using the sorted BAM file and reference FASTA.

```bash
samtools tview aln.sorted.bam ref.fasta
```

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

### Convert BAM to CRAM with samtools view

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

Shows two samtools view commands for converting BAM to CRAM. The first uses explicit CRAM version and options (decode_md=0, embed_ref, seqs_per_slice=2000), while the second uses the 'small' preset. Both write CRAM output files.

```bash
samtools view --input-fmt-option decode_md=0
    --output-fmt cram,version=3.0 --output-fmt-option embed_ref
    --output-fmt-option seqs_per_slice=2000 -o foo.cram foo.bam


samtools view -O cram,small -o bar.cram bar.bam

```

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

### samtools depth: Report per-base depth

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

Reports per-base depth of coverage from the sorted BAM file.

```bash
samtools depth aln.sorted.bam
```

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

### samtools quickcheck: Validate BAM/CRAM files

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

Quickly checks that the input files are valid BAM or CRAM files.

```bash
samtools quickcheck in1.bam in2.cram
```

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

### samtools fasta: Convert BAM to FASTA

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

Converts the input BAM file to FASTA format and writes to standard output.

```bash
samtools fasta input.bam > output.fasta
```

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

### Convert SAM to BAM with BAI index

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

Converts a SAM file to compressed BAM using BAI indexing. The --write-index option with the filename##idx##indexname notation specifies the index file name and format.

```bash
samtools view --write-index in.sam -o out.bam##idx##out.bam.bai

```

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

### Import SAM to BAM with @SQ header

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

Converts a SAM file to BAM when the header contains @SQ lines. The -b option outputs BAM format.

```bash
samtools view -b aln.sam > aln.bam
```

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

### samtools split: Split BAM by read groups

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

Splits the input BAM file into separate files based on read groups.

```bash
samtools split merged.bam
```

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

### Import SAM to BAM without @SQ header

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

Converts SAM to BAM when @SQ lines are absent. First generates the .fai index with faidx, then uses -t to specify the index file.

```bash
samtools faidx ref.fa
samtools view -bt ref.fa.fai aln.sam > aln.bam
```

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

### samtools stats: Report BAM statistics

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

Reports detailed statistics for the sorted BAM file.

```bash
samtools stats aln.sorted.bam
```

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

### Convert BAM to CRAM with local reference

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

Converts a BAM file to CRAM using a local reference sequence specified with -T.

```bash
samtools view -C -T ref.fa aln.bam > aln.cram
```

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

### samtools mpileup: Generate pileup for a region

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

Generates pileup for the specified region using the reference FASTA. The -f option specifies the reference and -r the region.

```bash
samtools mpileup -f ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
```

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

### samtools flagstat: Report flag statistics

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

Reports statistics on the flags in the sorted BAM file.

```bash
samtools flagstat aln.sorted.bam
```

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

### samtools ampliconstats: Compute amplicon statistics

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

Computes amplicon statistics from the given BAM file using the primer intervals in primers.bed.

```bash
samtools ampliconstats primers.bed in.bam
```

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

### Convert BAM to compressed SAM with CSI index

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

Converts a BAM file to compressed SAM with CSI indexing. The -h flag includes the header, -O sam,level=6 requests compressed SAM output, and --write-index creates an index automatically.

```bash
samtools view -h -O sam,level=6 --write-index in.bam -o out.sam.gz

```

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

### samtools reheader: Replace BAM header

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

Replaces the header of the input BAM file with the header from in.header.sam and writes the result to standard output.

```bash
samtools reheader in.header.sam in.bam > out.bam
```

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

### samtools idxstats: Report per-reference statistics

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

Reports statistics per reference sequence from the index of the sorted BAM file.

```bash
samtools idxstats aln.sorted.bam
```

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

### samtools merge: Merge BAM files

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

Merges multiple BAM files into a single output BAM file.

```bash
samtools merge out.bam in1.bam in2.bam in3.bam
```

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

### samtools targetcut: Cut BAM at target regions

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

Cuts the input BAM file at target regions.

```bash
samtools targetcut input.bam
```

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

### samtools checksum: Compute BAM checksum

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

Computes a checksum for the input BAM file.

```bash
samtools checksum in.bam
```

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

### samtools addreplacerg: Add or replace read groups

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

Adds or replaces read group tags in the input BAM file and writes the result to output.bam. The -r option specifies read group fields such as ID, LB, and SM.

```bash
samtools addreplacerg -r 'ID:fish' -r 'LB:1334' -r 'SM:alpha' -o output.bam input.bam
```

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

### samtools cat: Concatenate BAM files

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

Concatenates multiple BAM files into a single output BAM file. The input files must be in the same sort order.

```bash
samtools cat out.bam in1.bam in2.bam in3.bam
```

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

### samtools consensus: Generate consensus sequence

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

Generates a consensus sequence from the input BAM file and writes it to the specified FASTA file.

```bash
samtools consensus -o out.fasta in.bam
```

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

### samtools flags: Convert flag names to numeric value

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

Converts a comma-separated list of flag names to their numeric value.

```bash
samtools flags PAIRED,UNMAP,MUNMAP
```

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

### samtools fixmate: Fix mate information

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

Fixes mate information in a name-sorted SAM file and writes the result to a BAM file.

```bash
samtools fixmate in.namesorted.sam out.bam
```

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

### samtools sort: Sort BAM file

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

Sorts the input BAM file by coordinate and writes the result to the specified output file. The -T option specifies a temporary file prefix.

```bash
samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
```

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

### samtools view: Convert SAM to BAM

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

Converts a SAM file to BAM format. The -b option specifies BAM output, -t specifies a reference list file, and -o specifies the output file.

```bash
samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
```

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

### samtools collate: Collate reads by name

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

Collates reads by name and writes the result to the specified output file. The -o option specifies the output BAM file.

```bash
samtools collate -o aln.name_collated.bam aln.sorted.bam
```

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

### samtools cram-size: Estimate CRAM file size

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

Estimates the size of a CRAM file. The -v option enables verbose output and -o specifies the output size file.

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

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

### samtools ampliconclip: Clip reads to amplicon intervals

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

Clips reads to the amplicon intervals defined in the BED file. The -b option specifies the BED file containing the amplicon regions.

```bash
samtools ampliconclip -b bed.file input.bam
```

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

### samtools reference: Extract reference from CRAM

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

Extracts the reference sequence from a CRAM file and writes it to the specified FASTA file.

```bash
samtools reference -o ref.fa in.cram
```

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

### samtools calmd: Calculate MD tags

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

Calculates and adds MD tags to the sorted BAM file using the reference FASTA file.

```bash
samtools calmd in.sorted.bam ref.fasta
```

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

### samtools markdup: Mark duplicate reads

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

Marks duplicate reads in the input BAM file and writes the result to the output BAM file.

```bash
samtools markdup in.algnsorted.bam out.bam
```

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

### samtools reset: Reset alignment information

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

Resets the alignment information in the input BAM file and writes the result to the specified output file.

```bash
samtools reset -o /tmp/reset.bam processed.bam
```

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

### samtools bedcov: Report per-interval coverage

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

Reports the depth of coverage per genomic interval from the sorted BAM file.

```bash
samtools bedcov aln.sorted.bam
```

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

### samtools depad: Remove padding from BAM

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

Removes padding from the input BAM file.

```bash
samtools depad input.bam
```
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