madzayasodara
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Recent activity by madzayasodara Sort by recent activity-
USER ERROR has occurred: Sorry, we only support a single reads input for for this spark tool.
When I run gatk HaplotypeCallerSpark -R newzf20/GCF_008822105.2_bTaeGut2.pat.W.v2_genomic.fa -I RSFV1A_match.bam -I RSFV1B_match.bam -L NC_044998.1 --stand-call-conf 30 -mbq 20 --spark-runner LOCA...
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Which exact info does BaseRecalibrator uses from a vcf?
I'm wondering if I can use a vcf generated from ANGSD to recalibrate bases using BaseRecalibrator. Which info the program actually extract from the vcf to run the recalibration? ANGSD vcf output h...
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HaplotypeCaller mem/cpu/threads/node specs
Hi I'm running HaplotypeCaller to call raw variants for each chr in whole gen seq data for 23 individuals (tot gen size ~1.2G, coverage ~10x/ind) but it's certainly taking very long (more than 2 da...
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HaplotypeCaller too many alternative alleles found
AnsweredHi I'm calling raw variants with the intent of using them for base re-calibration and have noticed that for some sites HaplotypeCaller gives me this warning. I have whole genome seq data for 23 di...