Hi,
I am using the following command
(samtools view -bS $prefix.out.sam > $prefix.out.bam
samtools sort $prefix.out.bam $prefix.out-sorted
samtools rmdup $prefix.out-sorted.bam $prefix.out-sorted-NoDup.bam
samtools mpileup -ugf HumanRef-hg19.fa $prefix.out-sorted-NoDup.bam | bcftools view -bvcg - > $prefix.var.raw.bcf
bcftools view $prefix.var.raw.bcf | vcfutils.pl varFilter -D 100 > $prefix.var.flt.vcf
) &
to find SNPs with samtools mpileup.
All $prefix.out-sorted-NoDup.bam files get generated OK.
The problem I have is that the *.vcf files contain only chromosomes 1 to 3.
What can be the cause of this?
Thank you.
I am using the following command
(samtools view -bS $prefix.out.sam > $prefix.out.bam
samtools sort $prefix.out.bam $prefix.out-sorted
samtools rmdup $prefix.out-sorted.bam $prefix.out-sorted-NoDup.bam
samtools mpileup -ugf HumanRef-hg19.fa $prefix.out-sorted-NoDup.bam | bcftools view -bvcg - > $prefix.var.raw.bcf
bcftools view $prefix.var.raw.bcf | vcfutils.pl varFilter -D 100 > $prefix.var.flt.vcf
) &
to find SNPs with samtools mpileup.
All $prefix.out-sorted-NoDup.bam files get generated OK.
The problem I have is that the *.vcf files contain only chromosomes 1 to 3.
What can be the cause of this?
Thank you.
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