Hello,
I am trying to generate a vcf file from the following 1000 genomes sample:
CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam
I have gone through different iterations of all mpileup and bcftools options and the vcf file generated is consistently empty (even when I do not use -v) apart from the header lines. I have tried piping and doing it separately and nothing works.
I have successfully worked with other bam files (including other 1000 genome, though from different download directories), so I am beginning to think it may something specific about this file.
Has anyone else come across a similar issue, and how did they resolve it?
Thanks!
I am trying to generate a vcf file from the following 1000 genomes sample:
CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam
I have gone through different iterations of all mpileup and bcftools options and the vcf file generated is consistently empty (even when I do not use -v) apart from the header lines. I have tried piping and doing it separately and nothing works.
I have successfully worked with other bam files (including other 1000 genome, though from different download directories), so I am beginning to think it may something specific about this file.
Has anyone else come across a similar issue, and how did they resolve it?
Thanks!
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