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Old 01-12-2011, 11:59 AM   #1
Location: Bethesda

Join Date: Jul 2010
Posts: 15
Default samtools/bcftools problem?


I have exome data (single end reads from SoLiD). I am trying to call SNPs using bcftools with the following command

>bcftools view -vcG *.bcf >*.vcf

The *.vcf file only has indels and no SNPs

When I repeat it with just -c option, then the output file does not contain the alternate alleles?
>bcftools view -c *.bcf >*.vcf

Does anyone else have this problem?

Thank you.

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