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

Join Date: Sep 2012
Posts: 3
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'

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