Extract bed file of uwanted chromosome names and positions from bam file

Question

[tien]

Hello everyone,

Besides chr1->22, there are others name like chrM, KI270728.1,.... I want to create a bam file of these chromosome names (which is listed in common_chr.bed) by using samtools

samtools view -L common_chr.bed -U out_bam.bam in_bam.bam

I need to create common_chr.bed but not sure how to do this. Is there any way to create such bed file of distinct chromosome names and their positions from in_bam.bam that excludes chr1->22

Thanks for your help.

Answer 1

[Pierre Lindenbaum]

use the reference.fa.fai file create by samtools faidx

awk -F '\t' '($1 ~ /^(chr)?[0-9]+$/) {printf("%s\t0\t%s\n",$1,$2);}' reference.fa.fai > common.bed

[tien]

Thanks for your reply. I'm using output from cellranger and find no such fastq file for faidx. The two files that I have is bam and its bam index file. I try to use the above command with bam index file but it does not work. Do you know any other methods?

[Pierre Lindenbaum]

find the fasta reference file, index it with samtools faidx /path/to/ref.fasta