Hi, I am using bowtie + samtools pipeline to call snp. Split bam file and call snp by chromosome will save a lot of time.
But the reference genome have many scaffold, split bam by chromosome will produce a lot of scaffold_bam file. Now I want to split bam by scaffold, so the scaffold will split into one file.
Is there any way to do that?
I tried to use command:
samtools view in.bam scaffold1 scaffold2 -b > scaffold1_2.bam
but I don't know how to check if scaffold1_2.bam contains scaffold1 and scaffold2.
Thanks
1 answer
Maybe something on these lines?
First prepare a string of required scaffold names. You can extract all the scaffold names for the bam header and use grep to get only those matching a certain patter. In this example get only scaffolds starting with "chr1":
chroms=`samtools view -H in.bam \
| awk '$1 == "@SQ" {sub("SN:", "", $2); print $2}' \
| grep -P '^chr1.*'`
Then pass this string to samtools. If the string is really long, you might need xargs to split it otherwise you exceed the maximum length of a single command (assuming you are on *nixsystem):
echo $chroms | xargs samtools view -b in.bam > scaffold1_2.bam
(Not fully tested...)
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I've tried to do the command above, the output contains 2 scaffolds!
it works