Download the latest Picard release at
GATK version 4.beta.5 is out. See the GATK4 beta page for download and details.

Calling SNPS/indel by unified genotyper


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


  • Hi

    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 Charlestown, MAMember

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

Sign In or Register to comment.