Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
HaplotypeCaller may fail to detect variant with the same reads with a different composition.
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different.
NextSeq2_point.bam: bam is composed of the reads which cover chr16: 89100686 position only.
NextSeq2_region.bam: bam is composed of the reads which cover the region of chr16: 89100686 +-100bp.
On position chr16:89100686, I presume T>C should be detected, but HaplotypeCaller failed to detect the variant with NextSeq2_region.bam.
chr16 89100686 . T C,<NON_REF> 7397.77 . DP=199;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=716400.00 GT:AD:DP:GQ:PL:SB 1/1:0,199,0:199:99:7426,599,0,7426,599,7426:0,0,155,44
chr16 89100686 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:0,199:199:0:0,0,0
What causes the difference and why?
--- GATK Version (Docker latest) Using GATK wrapper script /gatk/build/install/gatk/bin/gatk Running: /gatk/build/install/gatk/bin/gatk HaplotypeCaller --version Version:220.127.116.11 --- --- Command used gatk HaplotypeCaller -I /temp/NextSeq2_region.bam -O /temp/NextSeq2_region.vcf -R /temp/genome.fa -L /temp/only16.bed --debug true --output-mode EMIT_ALL_SITES --all-site-pls true --dont-trim-active-regions true --emit-ref-confidence BP_RESOLUTION --- --- Genome Version: hg38 --- bed chr16 89100681 89101347 NM_174917.4_cds_2_0_chr16_89100682_f 0 +
If you need the bams and vcfs, I can post them here.