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Old 09-05-2012, 06:53 AM   #1
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Location: Hannover

Join Date: Sep 2012
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Default samtools/bcftools: How to inspect SNPs not made it into vcf file


Is there any parameter to "log" the snp-calling for individual SNP's which did not make it into the .vcf ? Or any other way to look how are the parameters for that SNP, if called ?

Info: We generate our vcf's like this:

samtools mpileup -ugf 'human_build37_ucsc.fa' 'test.bam' | bcftools view -bvcg - > 'test.bam.bcf'
bcftools view 'test.bam.bcf' > 'test.bam.bcf.vcf'

muenalan is offline   Reply With Quote
Old 09-06-2012, 01:46 AM   #2
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Location: Germany

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I'm not sure if I understand your question correctly.

In general, omitting the "-v" in bcftools will show you all positions, not just the variants.

A convenient way to manually inspect a single position that didn't get called is the "samtools mpileup -r" option, where eg "samtools mpileup -r CHROMOSOMEII:10-10 ..." will show you only this one location.

If you are talking about doing this in bulk for the whole genome, a possibility is to do a second pileup of all positions and then find the differences via "diff" or a custom script.

Hope to help,

AWeller is offline   Reply With Quote
Old 09-06-2012, 05:13 AM   #3
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Default [solved]


Exactly the information I was looking for.

muenalan is offline   Reply With Quote

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