Hello all,
I am trying to process whole exome sequencing data from a CT26 cell line, using the balb/c genome as reference.
When I started off, my known sites vcf file had mismatching contigs with my balb/c reference genome, so I used picard UpdateVcfSequenceDictionary to generate a new vcf known sites file to match the reference genome.
After that, I proceeded with the remaining steps using tumor-only mode: bwa-mem2 on the raw reads, indexing and sorting with samtools, MarkDuplicatesSpark, BQSR, ApplyBQSR, and finally Mutect2 to call the final variants.
After obtaining the final vcf file, I filtered using FilterMutectCalls with no additional parameters apart from input file and output file, but this gave me an empty file. Does this indicate that the filters were too stringent, or there was something wrong with my entire process? Any pointers would be greatly appreciated.
do you mean there was no variant or the file was just empty ? Show us the command line as well as the warnings log messages when the last file was created.
Nevermind, sorry. I figured out the issue. It was that I had moved the .stats file to another directory.