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
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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