
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"
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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...
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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_...
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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?
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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 \-...
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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 ...
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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...