Li Tai Fang

Can you try the following somaticseq command, to see what's in the bam files for your snv/indel positions? If you have the latest SomaticSeq v3.4.0 installed, `somatic_vcf2tsv.py` is in your...

Looking at the two tsv.txt files, it's not obvious to me why the four callers are all "negative" for all the variant positions. Column #6, 7, 10, and 14 are...

Thanks for pointing that out to me. Some calls outside the high confidence regions were left in those files. I'll make a note of that in README and release corrected...

SEQC2 has an update with `README.md` there explaining the differences (and why): https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/

Thanks for letting me know. I put java back into `lethalfang/somaticseq:latest`.