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RN Sarma

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Latest activity by RN Sarma
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    RN Sarma created a post,

    GenomicsDBImport cannot use multiple VCF reader threads for initialization when the number of intervals is greater than 1. Falling back to serial VCF reader initialization.

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    2. General Discussion

    GATK version; 4.5 The code is:  GENOMICSDB_PATH="$OUTPUT_DIR/my_genomicsdb" gatk --java-options "-Xmx60G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" GenomicsDBImport \    -R "$REFERENCE_GENOME" \    ...

    • RN Sarma
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    RN Sarma created a post,

    No output from GATK

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    2. New User Advice

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

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    RN Sarma created a post,

    GATK Command for variant discovery

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    2. New User Advice

    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...

    • RN Sarma
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    RN Sarma commented,

    1. Community
    2. New User Advice
    3. GenomiCDBImport issue

    The usage of gatk GatherVcfs is:gatk GatherVcfsCloud \     -I cohortA_chr1.vcf.gz \     -I cohortA_chr2.vcf.gz \     -O cohortA_chr1chr2.vcf.gz 1. Why is there is GAtherVcfCloud, as my output files...

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    RN Sarma commented,

    1. Community
    2. New User Advice
    3. GenomiCDBImport issue

    My script, as shown below, has produced folders  like "genomicsdb_1" to "genomicsdb_11" in the directory "/home/rnsarma/Desktop/Mungbean/Combined_GVCF".  How to get one VCF file for all chromosomal...

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    RN Sarma commented,

    1. Community
    2. New User Advice
    3. GenomiCDBImport issue

    Java version: openjdk version "11.0.23" 2024-04-16OpenJDK Runtime Environment (build 11.0.23+9-post-Ubuntu-1ubuntu122.04.1)OpenJDK 64-Bit Server VM (build 11.0.23+9-post-Ubuntu-1ubuntu122.04.1, mix...

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    RN Sarma commented,

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    2. New User Advice
    3. GenomiCDBImport issue

    The script ended abruptly with this line at the end " A USER ERROR has occurred: genomicsdb-workspace is not a recognized option ********************************************************************...

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    RN Sarma created a post,

    GenomiCDBImport issue

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    2. New User Advice

    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_...

    • RN Sarma
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    RN Sarma created a post,

    Consolidating GVCF

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    2. General Discussion

    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?

    • RN Sarma
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    RN Sarma created a post,

    Idetify biallelic loci in GATK 4,8

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    2. General Discussion

    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 \-...

    • RN Sarma
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