Zev Kronenberg
Zev Kronenberg
I only work on my OS X. brew install htslib, nim develop, and htsnim.
@JuanmaMedina, Depending on your use case whamG might better choice. WhamG internally classifies structural variant types, and is generally more accurate. However, if you need to classify wham calls, I'll...
-s requires that both the start and end of two SV be no more than S base pairs apart. At -s 100 if the two start positions are at 1000...
That is really, really bizarre. Does this happen on clean install?
Thank you kindly
Odd. Can you post the full error message? This is whole genome paired end sequencing data? Also, can you post the header of the bam file? Specifically, do you have...
can you post the full SL150028.err error file? There should be something like: INFO: for Sample:xxx STATS: UV940: mean depth ..............: 39.2523 STATS: UV940: sd depth ................: 10.7403 STATS: UV940:...
@afkoeppel thanks, I was expecting it to be longer, but maybe not if it is an options parsing error. original: "whamg -a $GENOME **–**f SL150028.bwamem.unfilt.rmdup.sort.bam > SL150028.vcf 2> SL150028.err" try:...
Shame on me! I'll make sure to check for m vs n dash. http://www.punctuationmatters.com/hyphen-dash-n-dash-and-m-dash/ The wrong dash was in the README.
Currently It does not support BND or TRA. I will be working on it over the next couple weeks. --Zev