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Calling SNPS/indel by unified genotyper

opulcyopulcy Posts: 15Member


I was using GATK UnifiedGenotyper for SNPs/indels. My command is as follows:

java -Xmx16g -jar $gatkPath/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R $humanRefSequence \ -I "$sampleID".recal.bam \ --dbsnp $humanDbsnpFile \ -stand_call_conf 30.0 \ -stand_emit_conf 10.0 \ -dcov 250 \ -l INFO -log "$sampleID".GATKvariants.log \ -o "$sampleID".GATKvariants.raw.vcf \ --output_mode EMIT_ALL_SITES

When I am selecting Indels from the vcf file, it's producing an empty vcf file (which is working fine with SNPs). My command for selecting Indels are as follows:

java -Xmx10g -jar $gatkPath/GenomeAnalysisTK.jar \ -T SelectVariants \ -R $humanRefSequence \ --variant "$sampleID".GATKvariants.raw.vcf \ -o "$sampleID".GATKindels.raw.vcf \ -selectType INDEL \ -log "$sampleID".SelectIndels.log

Do I need to use "-glm BOTH" in UnifiedGenotyper to output both SNPs and Indels? As from the documentation, I understand that the default value of -glm is set to SNP.

Many thanks in advance.

Best Answer


  • drashu_11drashu_11 Posts: 10Member


    I have 4 GATK recalibrated bamfiles for cow genomic sequences I call SNP for multiple bam files using GATK UnifiedGenotyper by following command

    $java -Xmx100g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R umd3.1_genome.fa -I Sample_1_rcal.bam -I Sample_2_rcal.bam -I Sample_3_rcal.bam -I Sample_4_rcal.bam --dbsnp cow_dbsnp133_snps_indels.vcf -o snps.raw.vcf --min_base_quality_score 30 -stand_call_conf 50 – stand_emit_conf 10 -dcov 200

    I tried twice by rearranging the postion of input files, but each time I have output file with only 3 samples

    I need help to overcome this problem

    Thank you

  • CarneiroCarneiro Posts: 271Administrator, GSA Member admin

    maybe two of your files have the same sample tag in the read group?

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