Refseq Number/Name In Bam File
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8.1 years ago

I am using bamread in matlab to read a bam file that I downloaded from 1000G. In the website it says all the reads are mapped to reference sequence called "GRCh37" which make sense. But when I try to read it in matlab, it's syntax is

bamread(File,RefSeq,Range)

The problem is this RefSeq in bamread, doesn't recognize "GRCh37" whatsoever! then I tried to pass refseq code such as 1 or 2 or ... it works but I think I'm missing sth. How do I make sure that the reads are exactly mapped to reference GRCh37 while I don't see it in the bam file?

Thanks in advance!

reference sequence bam read • 2.3k views
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The point of confusion seems to be that GRCh37 is not a single sequence but multiple chromosomes which are usually named in bam files as 1, 2, ..., 22, X, Y

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8.1 years ago

print the header of your bam with samtools:

samtools view -H  file.bam |  grep '^@SQ'

the chromosomes contained in your reference will be listed there.

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