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The format column of my VCF file (Generated by PostprocessGermlineCNV) contains GT:CN:NP:QA:QS:QSE:QSS. GT - Genotype CN - Copy Number What do the rest of the acronyms mean? I've tried looking at the documentation and other forums, but couldn…
Worked like a charm! Thanks!
Just to follow-up: Splitting the 420k intervals into 17 shards of ~25k intervals each seems to work well! Thanks for the help!
Thanks @slee and @bhanuGandham! If I use the scatter option from IntervalListTools, how large would you suggest I set the 'scatter content' to, given that I have about 420k intervals and 16Gb memory? Also if scattered into multiple interval f…
Hi @bhanuGandham, Thanks for the heads-up. Will check this out!
#COMMAND: ''' gatk GermlineCNVCaller --run-mode COHORT -L my_data/Ancestry_004_probes_hg19.excludedline.bed --interval-merging-rule OVERLAPPING_ONLY --contig-ploidy-calls contig_ploidy_out/201to221-calls/ --input my_data/201.counts.tsv --input my_…
Hi @bhanuGandham ! There is an error towards the bottom: ``` Stderr: at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75) at org.broadinstitute.hellbender.utils.runtime.ScriptExecuto…
Could it be because I'm using only 20 samples instead of 100+ ?