hguturu
commented
7 years ago I noticed these types of issues in a batch of variant calls I received from Illumina as well. It is tagged with
source=IsaacVariantCaller
source_version=starka-2.1.4.2
Is there any idea what is causing the caller to call hemizygous variant calls on autosomes?
Hi, there. I'm user of Isaac aligner and isaac variant caller. I realigned Hiseq reads by Isaac aligner and then called variant by isaac variant caller with following commands.
isaac-align -r /path to/iSAACIndex.hs37d5/sorted-reference.xml --base-calls-format fastq-gz -b /path to/Run_01 -o /path to/sample001/ -t /tmp -j 30 -m 120
configureWorkflow.pl \ --bam=/path to/sorted.bam \ --ref=/path to/hs37d5.fa \ --config=/path to/isaac_variant_caller-v1.0.6/etc/ivc_config_default.ini \ --output-dir=/path to/isaac_variant_caller/;
make -j 40 -C /path to/isaac_variant_caller/ 1> log 2> err;
As a result, I got sorted.genome.vcf.gz file. In this file, I found unexpected value "1" in GT field as follows,
22 22536804 . T C 207.0 PASS SNVSB=-24.6;SNVHPOL=2;SNP;HOM;VARTYPE=SNP GT:GQ:GQX:DP:DPF:AD 1:33:33:12:1:0,12 22 23568516 . T A 331.0 PASS SNVSB=-34.0;SNVHPOL=3;SNP;HOM;VARTYPE=SNP GT:GQ:GQX:DP:DPF:AD 1:66:66:23:3:0,23 22 27436971 . T A 224.0 PASS SNVSB=-28.9;SNVHPOL=6;SNP;HOM;VARTYPE=SNP GT:GQ:GQX:DP:DPF:AD 1:36:36:13:1:0,13
I expected these GT value should be "1/1" because of AD value.
I counted these unexpected value in gVCF file as follows. zcat sorted.genome.vcf.gz | grep -v "^#" | awk '{print $10}'|awk -F: '{print $1}' | sort | uniq -c 866614 . 248249 0 394681299 0/0 2662537 0/1 3021 1 1871600 1/1 21859 1/2
Although "." would be derived from gVCF annotation, I found 3021 "1" value in GT field. VCF-merge by VCFtools was failed by this unexpected value with the extracted VCF files from these gVCF files.
I would like to know why these unexpected values are existed in my files. Does Someone know answer for this unexpected value ?
isaac version isaac_aligner-01.15.02.08 isaac_variant_caller-v1.0.6