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Old 06-14-2017, 10:32 AM   #1
MGCBrown
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Location: Canada

Join Date: May 2017
Posts: 15
Question samtools SNP calling pipeline outputs VCard file instead of variant call format (VCF)

Hello,

I used this workflow to call SNPs on bam files that were aligned to a reference de novo transcriptome assembly:

samtools mpileup -uf normalized_Trinity.fasta aln2.bam aln2.bam | bcftools view -bvcg \
- > var.raw.bcf

bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf



However, the final var.flt.vcf output is a VCard file in my Bitvise ssh client.

Any insight as to why this might be would be greatly appreciated!

Thanks,

Mike
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