Hi all,
I am working with exome reads, i extracted SNP and indels using,
# samtools mpileup -ugf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
# bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
i don't know what -D read depth means in vcfutils.pl?
i am having 101245 reads FYI.
I am working with exome reads, i extracted SNP and indels using,
# samtools mpileup -ugf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
# bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
i don't know what -D read depth means in vcfutils.pl?
i am having 101245 reads FYI.
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