-
RE: Query regarding picard liftoverVcf
#CHROM POS ID REF ALT QUAL FILTER INFO -
RE: Using JEXL to apply hard filters or select variants based on annotation values
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT @[email protected] @[email protected] -
Relative path in json files for cromwell
I have the following json file that has absolute path for all the files. -
Missing chr in gVCF
#CHROM -
Interpreting of CNV pipeline results
Dear GATK team, first af all thanks a lot for the very detailed manual for CNV calling it was super helpfull! -
ALT * no deletion
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OF1-M OF2-M OF3-M OF4-M OM1-M OM2-M OM3-M OM4-M -
RE: Meaning of warning (<10 samples for inbreeding calculation) while joint genotyping (GenotypeGVCFs)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H07738-L1 H07739-L1 H07740-L1 H07741-L1 H07742-L1 H07743-L1 H07744-L1 H07745-L1 H0774 -
RE: What is a GVCF and how is it different from a 'regular' VCF?
Hi, thanks for your comment I realize that the title of the graphs are not there so it is mixing. Here is the exact command that I ran to produce the last 2 graphs above: -
Call somatic short variants with mutect - BAM file contigs not matching the reference
Dear GATK Staff, -
RE: Do you need to do Variant Quality Score Recalibration when calling somatic variants with Mutect2?
