Cyriac Kandoth

icon indicating a website link https://linkedin.com/in/ckandoth icon indicating an email [email protected]

icon company Penn Medicine icon location Perth, WA, Australia icon location I'm an engineer that studies the pathogenesis of genetic diseases like cancer, in search of druggable targets, early diagnosis, and prevention.

Results 26 comments of Cyriac Kandoth

maf2vcf.pl: multiple FILTER tags should be semicolon separated

Thanks @soccin - I switched [from comma to semicolon in release `v1.6.14`](https://github.com/mskcc/vcf2maf/releases/tag/v1.6.14), but this looks like an unhandled exception when the input MAF uses commas, and is copied unchanged. I'll...

how to run vcf2maf with clinvar db

You are using VEP, not vcf2maf. But I'll try to help. If all the variants are showing as intergenic, then it is likely that you are using a transcript/reference that...

Empty 't_depth' 't_ref_count' 't_alt_count'

Your VCF looks fine. But make sure that "tumor-id" exactly matches the name of the sample ID in your VCF column header for th genotype field. This is needed to...

'align_to_contig.sam.sai' : No such file or directory

I'd also recommend switching to the latest version of BWA. [This thread](http://sourceforge.net/p/bio-bwa/mailman/message/32590409/) mentions a critical bug in BWA 0.7.9a-r786.

Remove --af_esp flag as it's deprecated

Thanks for this. Unfortunately, vcf2maf's output became the [standard MAF format](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) that includes two columns for these ESP allele frequencies. So, we'll leave the columns in, but it will never...

Support both HDFS and NFS/other file systems for BAM files

I'm testing out Cycledash as a way to compare test/truth VCFs, and to easily view discordant calls in IGV. Since our BAMs are not in HDFS, this issue seems to...