Tumor only BAM files for mpileup or varscan

[adrian]

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

[2nelly]

How did u run MuTect using no control?Try Haplotypecaller or UnifiedGenotyper.

That way, you will discover both types germline and somatic mutations.

Then you need to filter out germline mutations using dbsnp and a panel of normals
Also you need to filter out false positives calls (read GATK documentation) like putting thresholds for coverage, strand bias etc.

The difference you see in the outputs of those two tools, it is mostly due to different variant filtration process.
Of course every algorithm has some differences, but in snv detection all tools more or less give nicely overlapping outputs.

In any case, it s practically impossible to get 100% match using both tools (different algorithms). According to your prediction what is the overlap u get?