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Abrish

  • Total activity 63
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  • Query regarding Intervals and interval lists for Target Enrichment Sequecing

    Answered

    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 Caller

    Answered

    /home/anaconda3/share/gatk4-4.2.4.0-0/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...

  • gatk4-4.2.4.0-0 Fixmate Error

    Answered

    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...

  • ValidateSamFile Error

    Answered

    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-4.1.9.0/gatk ValidateSamFile --java-opt...

  • Queey regarding Read group effect on Haplotype caller and Pipeline steps

    Answered

    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 CombineGVCFs

    Answered

    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 bostau6

    Answered

    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 genome

    Answered

      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...