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-   -   samtools SNP calling pipeline outputs VCard file instead of variant call format (VCF) (http://seqanswers.com/forums/showthread.php?t=76574)

MGCBrown 06-14-2017 10:32 AM

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

HESmith 06-14-2017 11:44 AM

It's not actually VCard format. It's just that VCard uses the same file extension (.vcf) as VCF, and your computer is configured to read the former by default. Open the VCF in a flat text editor and you'll see.

Brian Bushnell 06-14-2017 04:38 PM

For a Windows text editor, I recommend Notepad++. Though normally I find Excel slightly easier for VCFs, if they are small enough.

MGCBrown 06-15-2017 05:55 AM

Thanks for the help! I see that when I open my ssh client on a different computer, the files are no longer using the VCard extension.

Thanks again.


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