How to split SAM file to different chromosomes

Question

[javanokendo]

I have a SAM file which I now want to split into different chromosome from chromosome chr1..chr20 as follows.

/home/SpliceGraph/Human/chr1.sam
/home/SpliceGraph/Human/chr2.sam/
/home/SpliceGraph/Human/chr3.sam/
/home/SpliceGraph/Human/chr4.sam/
/home/SpliceGraph/Human/chr5.sam

Which command can I use to do this?

[ATpoint]

How To Split A Bam File By Chromosome

[javanokendo]

The following code: samtools idxstats out.bam | cut -f1 | grep -v '*' > chr.names is not giving the list of chromosomes. It give something like this:

NC_000001.11
NT_187361.1
NT_187362.1
NT_187363.1
NT_187364.1
NT_187365.1
NT_187366.1
NT_187367.1
NT_187368.1
NT_187369.1
NC_000002.12
NT_187370.1
NT_187371.1
NC_000003.12
NT_167215.1
NC_000004.12
NT_113793.3
NC_000005.10
NT_113948.1
NC_000006.12
NC_000007.14
NC_000008.11
NC_000009.12
NT_187372.1
NT_187373.1
NT_187374.1
NT_187375.1
NC_000010.11
NC_000011.10
NT_187376.1
NC_000012.

[GenoMax]

Those are the chromosome (reference) names that are present in your BAM file.

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[ATpoint]

Please use ADD COMMENT to reply to answers. It gives you the names that were in the fasta file that you mapped against. The command itself is correct. If you want different names then align against a fasta file that contains the names you would like.

Answer 1

[ATpoint]

## Convert SAM to BAM and index it:
samtools view -o out.bam in.sam
samtools index out.bam

## Extract chromsosome names:
samtools idxstats out.bam | cut -f1 | grep -v '*' > chr.names

## Split bam file with w while loop
while read p
  do
  samtools view -o out_${p}.bam out.bam ${p}
  done < chr.names

If you really want SAM instead of BAM files then use samtools view -ho out_${p}.sam out.bam ${p}. Given you have the resources you can of course use something like GNU parallel instead of a loop to make it more efficient.