Checking of GATK script

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RN Sarma

• June 07, 2024 08:09

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 GATK jar /usr/local/bioconda3/envs/gbs/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/bioconda3/envs/gbs/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar --version
Picked up _JAVA_OPTIONS: -Xmx32768m
The Genome Analysis Toolkit (GATK) v4.5.0.0
HTSJDK Version: 4.1.0
Picard Version: 3.1.1

The code:

gatk HaplotypeCaller \ -R /home/rnsarma/Desktop/Mungbean/mungbean_genome/Vigna_radiata.Vradiata_ver6.dna.toplevel.fa \ -I C1.sorted.bam -I C2.sorted.bam -I C3.sorted.bam -I C4.sorted.bam \ -I V100.sorted.bam -I V101.sorted.bam -I V102.sorted.bam -I V103.sorted.bam \ # ... (continue with the rest of your input files) ... -O ../raw_variants_mungbean_new_slurm_1.vcf \ -G StandardAnnotation \ --output-mode EMIT_ALL_CONFIDENT_SITES \ --max-alternate-alleles 1 \ --filter-indels \ # This line is added to remove indels --tmp-dir /var/tmp

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• 

  Gökalp Çelik

  • June 07, 2024 09:11

  Hi RN Sarma

  There are multiple issues with this commandline based on your purpose. 

  1- HaplotypeCaller does not have a parameter named and therefore using it will throw an error message.

  --filter-indels 

  If you wish to filter INDELS and just get SNPs then you can use 

  gatk SelectVariants --select-type SNP

  to get SNP calls only. 

  2- The below parameter will not return only biallelic sites but it will limit the number of called alternate alleles per loci to 1 and will drop all other alleles if there are more present. If you wish to get only biallelic sites then you may drop this parameter as well and just call variants and perform variant selection using the tool that I mentioned above to get what you exactly need. 

  --max-alternate-alleles 1

  I hope this helps. 

   

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