Hi group,
I have ~100 tumor only BAM files from miSeq using panel of 20 genes amplicons. I used a GATK pipeline with mutect2 with tumor only option.
I want to run mpileup too and verify the agreement of SNVs and indels.
I used mpileup the following way:
samtools mpileup -BQ0 -d 20000000 -uf /genomes/references/BWA/data/UCSC/sequence/ucsc.hg19.fasta T1_sort.bam | bcftools view - > T1.bcf
bcftools view T1.bcf | vcfutils.pl varFilter -D10000 > var.flt.vcf
Doing this way I cannot find the SNVs I found using GATK pipeline.
Any help appreciated.
Thanks
Adrian
I have ~100 tumor only BAM files from miSeq using panel of 20 genes amplicons. I used a GATK pipeline with mutect2 with tumor only option.
I want to run mpileup too and verify the agreement of SNVs and indels.
I used mpileup the following way:
samtools mpileup -BQ0 -d 20000000 -uf /genomes/references/BWA/data/UCSC/sequence/ucsc.hg19.fasta T1_sort.bam | bcftools view - > T1.bcf
bcftools view T1.bcf | vcfutils.pl varFilter -D10000 > var.flt.vcf
Doing this way I cannot find the SNVs I found using GATK pipeline.
Any help appreciated.
Thanks
Adrian
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