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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

VariantFiltration Invalid Argument

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    Bhanu Gandham

    Hi mons7re

     

    What is the QA field you are filtering on? Is that field present in your vcf?

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    mons7re

    I think so. Here is a row of my vcf:

    AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=7.35324;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.5789;NS=1;NUMALT=1;ODDS=13.3916;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=633;RO=19;RPL=1;RPP=3.0103;RPPR=12.2676;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=8.61041;SRR=13;TYPE=snp;technology.illumina=1

     

    Is there a better tool to filter quality, AC, AF and DP? I'm sorry if I am asking stupid questions, I am not experienced in bioinformatics, just working on a project!

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    Bhanu Gandham

    Can you please provide the header and the first few records of the vcf file? This does not look right. Here is what a vcf format looks like: https://samtools.github.io/hts-specs/VCFv4.2.pdf

     

     

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