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Genome Information From Bam

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

genomics chip-seq bam
• 1,934 views • link
updated by Pierre Lindenbaum 17K • | written by ChIP 60

1 answer

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
• 0 views • link
updated by Ram 4.5K • | written by Pierre Lindenbaum 17K

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