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Query regarding Intervals and interval lists for Target Enrichment SequecingAnswered
https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists Intervals and interval lists: As it has been mentioned in the given above link article that (the interval...
Query regarding Haplotype CallerAnswered
/home/anaconda3/share/gatk4-188.8.131.52-0/gatk HaplotypeCaller --java-options -Xmx100g -R genome.fa -I fixed.bam -O NmMdAndUqTag_fixed.g.vcf.gz -ERC GVCF --minimum-mapping-quality 20 --min-base-quali...
gatk4-184.108.40.206-0 Fixmate ErrorAnswered
I would be grateful If I could get help regarding this error. shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngineINFO: Failed to detect whether we are running o...
Hi GATK community, I had run the GATK pipeline on Ubuntu 18 version and I had also checked the VAlidateSamFile, then there was no error. /home//Software/gatk-220.127.116.11/gatk ValidateSamFile --java-opt...
Queey regarding Read group effect on Haplotype caller and Pipeline stepsAnswered
Dear Genevieve Brandt (she/her) and GATK community, I would like to know regarding the effect of read group on Haplotype caller. Here, I have shown an example, I have more samples in the same sc...
Query regarding CombineGVCFsAnswered
Hi Genevieve Brandt (she/her) and GATK community, I would like to know about the issue regarding CombineGVCFs. When I am trying to combine all vcf files together using CombineGVCFs as you can se...
Picard liftover Issue bostau8 to bostau6Answered
Hi, I want to liftover vcf file from bostau8 to bostau6 version. But I am getting this error and resulted file is empty. Kindly help me with this issue. java -jar /home/Software/picard/build/lib...
How to merge approx 150 bam file using Picard
Hi, I have checked everywhere, but I did not find any solution. It would be really appreciable if you could tell me that how to merge approx 150 bam files using MergeSamFiles Picard.
Error Creatting Dictionary for genomeAnswered
java -jar picard.jar CreateSequenceDictionary R=Bos_taurus_UMD_3.1.1_genome/Bos_taurus_NCBI_UMD_3.1.1/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/genome.fa O=Bos_taurus_UMD_3.1.1_gen...