Li Tai Fang
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`.
Yeah thanks for the report. ntree_limit has been deprecated in xgboost. Let me figure out what's the best way forward.
Thanks. iteration_range was introduced in v1.4. Think I'll make it `xgboost>=1.4`.
Do you know where did the data get unexpected Inf or NaN?
Looked around on internet it seems people have gotten that error when there are very large number (e.g., 1e300) in the data: https://stackoverflow.com/questions/67986268/xgboost-check-failed-valid-input-data-contains-inf-or-nan
Hmm, maybe because DP4 and VAF has quality filters (e.g., minimum mapping quality or base call quality) that a mutation caller used to make that call.