mpileup | bcftools 1000 genomes - empty vcf

[cdias]

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!

[DZhang]

Can you share your commands? A little dot is what it takes to give you an empty file.

Best regards,
Douglas

https://www.contigexpress.com

[cdias]

Among other iterations:

samtools mpileup -uf human_g1k_v37.fasta CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam | bcftools view > output

samtools mpileup -uf human_g1k_v37.fasta CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam | bcftools view -v > output

samtools mpileup -uf human_g1k_v37.fasta CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam | bcftools view -bvcg > output

samtools mpileup -u CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam | bcftools view -v > output