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Question: Genome Information From Bam

5.8 years ago by

ChIP • 550

Netherlands

ChIP • 550 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 • 1.2k views

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modified 5.8 years ago by Pierre Lindenbaum ♦ 125k • written 5.8 years ago by ChIP • 550

5.8 years ago by

Pierre Lindenbaum ♦ 125k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 125k 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 3 months ago by RamRS ♦ 25k • written 5.8 years ago by Pierre Lindenbaum ♦ 125k

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