Find single mutation with unified genotyper
Posted in Ask the GATK team | Last updated on 2013-07-22 19:56:55

Comments (20)

Hi, I try to find a single mutation with unified genotyper but can't find it. In my sample (human gene SOD1 from chr21) I removed the stop codon by 2 deletions. Than i run UnifiedeGenotyper as follows:

java -Xmx4g -jar ../GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ../human_g1k_v37.fasta -I test/chr21_SOD1_ENSG00000142168_removedStop_DEL_2_at_33040889.bwa.bam -o test/chr21_SOD1_ENSG00000142168_removedStop_DEL_2_at_33040889.bwa.raw.indels.vcf -D ../dbsnp_137.b37.vcf -nt 2 -glm INDEL -stand_emit_conf 10 -stand_call_conf 10 -deletions -1 -L test.intervals.bed

The resulting .vcf-file contains only the header but no results.

I played with the following parameters, but with no success.

Parameters are:

--indelGapOpenPenalty 5 -minIndelFrac 0 --min_indel_count_for_genotyping 1 -dt NONE --genotyping_mode GENOTYPE_GIVEN_ALLELES --output_mode EMIT_ALL_SITES

What could I do to find my mutation?

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