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  • samtools/bcftools problem?

    Hi,

    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.

    Nirmala

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