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Question: Genome Information From Bam
0
gravatar for ChIP
6.8 years ago by
ChIP • 580
Netherlands
ChIP • 580 wrote:

Hi!

Is their a way to know the genome build(ie., hg18 or hg19) to which the BAM file is aligned, other than manual inspection.

Thank you
bam chip-seq genomics • 1.3k views
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modified 6.8 years ago by Pierre Lindenbaum ♦ 132k • written 6.8 years ago by ChIP • 580
1
gravatar for Pierre Lindenbaum
6.8 years ago by
Pierre Lindenbaum ♦ 132k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 132k wrote:

get the dictionary in the sam header and test one chromosome

$ samtools view -H file.bam |\
 grep -E 'SN\:(chr)?22' |\
 awk '{if(index($0,"LN:51304566")!=0) printf("hg19\n"); else if(index($0,"LN:49691432")!=0) printf("hg18\n"); else printf("??\n");}'
hg19
ADD COMMENT • link modified 15 months ago by _r_am ♦ 32k • written 6.8 years ago by Pierre Lindenbaum ♦ 132k
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