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nimmi 01-12-2011 11:59 AM

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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