madzayasodara
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Latest activity by madzayasodara-
madzayasodara created a post,
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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madzayasodara commented,
Hello Genevieve Brandt (she/her) I managed to get rid of that error. I forgot to module load the needed python version and source my env in my slurm submission module load python/3.7.4source ~/Pys...
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madzayasodara commented,
Hello Genevieve Brandt (she/her), gotcha. Just few things I'm confused. There's no bam/sam file before this one I tested. Before that, I had fastq files I aligned with BWA. I also noticed this in ...
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madzayasodara commented,
Hi Genevieve Brandt (she/her) I checked the bam files I had generated by aligning my reads using bwa mem -R '@RG\tID:firstrun\tSM:RSFV1A\tPL:illumina\tLB:lib1\tPU:005' -p newzf20/GCF_008822105.2_b...
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madzayasodara commented,
Thank you :) This is weird my vcf check fails even when I call variants using HaplotypeCaller This is the cmd I use to call gatk HaplotypeCaller -R GCF_008822105.2_bTaeGut2.pat.W.v2_genomic.fa -I ...
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madzayasodara created a post,
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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madzayasodara commented,
Gotcha! Thanks
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madzayasodara commented,
See if I understood: GATK4 HaplotypeCaller can't multithread like GATK3 HaplotypeCaller, as GATK4 HP won't accept neither options -nct or -nt. The multithreading version of GATK4 HaplotypeCaller is...
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madzayasodara commented,
Not the same but related. It seems that yes if I am doing -nct 4, and request -c 4 in my SlLURM submission, the program will do one thread per core and performance will scale accordingly. Thank you
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madzayasodara commented,
Hello, yeah still get the same error either by using HaplotypeCaller or HaplotypeCallerSpark Error: Failed to load org.broadinstitute.hellbender.Main: org/apache/logging/log4j/core/appender/Abstrac...