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RN Sarma

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  • No output from GATK

    gatk HaplotypeCaller \        -R "$REFERENCE_GENOME" \        -I "$BAM_FILE" \        -O "$GVCF_FILE" \        -ERC GVCF \        -G StandardAnnotation \        --tmp-dir "$TMP_DIR"

  • GATK Command for variant discovery

    Is the script correct for GTK version 4.5 for SNP discovery?   #!/bin/bash#@(#)GATK_4.50-slurm_bioconda3_rns.sh  2025-01-06 R.N.Sarma # Define pathsREFERENCE_GENOME="/home/rnsarma/Desktop/Tea_Reseq...

  • GenomiCDBImport issue

    REQUIRED for all errors and issues: a) GATK version used:GATK4This script is asking me some more parameter.  Kindly check the script and suggest.   #!/bin/bash# "combined_GVCF_genomicDB_normal_rns_...

  • Consolidating GVCF

    GATK vesion 4.8 Which one should I use to to combine 107 GVCF of a diploid genome of 2n=450 Mb size, GenomicsDBImport or CombineGVCFs?

  • Idetify biallelic loci in GATK 4,8

    Is my codes correct to identify biallelic loci of  diploid genome? #!/bin/bash gatk HaplotypeCaller \-R /home/rnsarma/Desktop/Mungbean/mungbean_genome/Vigna_radiata.Vradiata_ver6.dna.toplevel.fa \-...

  • Checking of GATK script

    Is this script will retain only biallelic loci and remove indels in gataGATKversion 4.5.0?  Organism is diploid, purpose is to identify bialelic SNP, not indels. gatk --version being used is:Using ...

  • GATG-4.8

    My little slurm script gives me very low number of variant. Please suggest how to improve my GATK script to catch all variants #!/bin/bash#@(#)GATK_4.50-slurm_bioconda3_rns.sh  2024-05-15  R.N.Sarm...