Using Batch Files in Swiss Army Knife for Mutect2 Pipeline

Nicole Powell

Hello, 

I'm using Mutect2 to call somatic mutations from the WES data. To do this, I have to convert the CRAM files to BAM. 

#Code to generate batch files

dx generate_batch_inputs --path "project-Gfxv5x0JqZG7QB7qP4bz923g:/Bulk/Exome sequences/Exome OQFE CRAM files/10/" -iin="(.*)_23143_0_0.cram$"

This creates 19 batch files ranging from dx_batch.0000.tsv - dx_batch.0018.tsv

#Code to alter structure, puts project and file IDs into brackets

head -n 1 dx_batch.0000.tsv > temp.tsv && tail -n +2 dx_batch.0000.tsv | awk '{sub($3, "[" $3 "]"); sub($4, "[" $4 "]"); print}' >> temp.tsv; tr -d '\r' < temp.tsv > new.tsv; rm temp.tsv

#Code to run job using Swiss Army Knife samtools

# Path to your TSV file containing CRAM file IDs and reference information

Batch_Tsv="temp.tsv"

# Destination folder for output BAM files

Output_Folder="project-ID:/Username/<Your_Folder>"

# Run Swiss Army Knife app using the batch TSV

dx run swiss-army-knife \

  --batch-tsv "$Batch_Tsv" \

  -icmd='samtools view -T "/mnt/project/Bulk/Exome sequences/Exome OQFE CRAM files/helper_files/GRCh38_full_analysis_set_plus_decoy_hla.fa" -L "/mnt/project/Nicole/DNMT3A_locus.bed" -b "$in_name" > "$in_prefix".bam' \

  --destination="$Output_Folder" \

  --priority normal \

  --instance-type mem1_ssd1_v2_x2 \

  --detach --yes

 

This will run 1 job per 1 file within that batch tsv file. Does anyone know how I can alter this pipeline to run 1 job per say, 50 files in the batch tsv? Or has any recommendations on alternatives ways to run this pipeline?

 

Comments

1 comment

Date Votes
  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hello Nicole,

    mutect2 should accept crams as input, see: https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2 

    I don't believe that samtools view can handle multiple crams at once. 

    Also by running 1 job per file, it should be possible to choose a smaller and often less costly instance.

    Thank you for getting in touch, I hope this has been helpful.

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