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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

FilterMutectCalls

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    Genevieve Brandt (she/her)

    Nejla Ozirmak Lermi .gz is a zipped extension. If you wish to have the file unzipped, you can use many different methods to unzip the file. GATK does not have a tool to unzip it. 

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    Nejla Ozirmak Lermi

    Genevieve Brandt thank you for answering my question. 

    Actually the problem was output files that FilterMutectCalls created.

    I copied  " *.vcf.gz?" file as "*.vcf.gz" using cp command.

    Then, annotation software accepted new files as input files and the program annotated the variants. 

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    Genevieve Brandt (she/her)

    Hi Nejla Ozirmak Lermi, could you verify that this issue exists in GATK 4.1.9.0 and also supply your complete command?

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    Nejla Ozirmak Lermi

    Hi Genevieve Brandt, GATK 4.1.9.0 didn't exist in our server yet, thus I couldn't verify this issue in GATK 4.1.9.0. Complete command is below.

    gatk FilterMutectCalls -R rheMac8.toplevel.fa -V NOL7.merged.unfiltered.somatic.vcf.gz --tumor-segmentation NOL7.segments.table --contamination-table NOL7.calculatecontamination.table --output NOL7.merged.filtered.somatic.vcf.gz

    Output files were NOL7.merged.filtered.somatic.vcf.gz?; NOL7.merged.filtered.somatic.vcf.gz?.idx; NOL7.merged.filtered.somatic.vcf.gz?.filteringStats.tsv

     

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    Genevieve Brandt (she/her)

    Nejla Ozirmak Lermi I would like to try to verify this issue on my end. Please submit a bug report following these instructions including all necessary files for the script to run, the command in a text file, and the error message in a text file.

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