Tagged with #iontorrent
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Recent thread: http://gatkforums.broadinstitute.org/discussion/1677/best-practice-for-variant-calling-on-ion-torrent-data-with-gatk

Any progress on some Best Practices for data processing pipelines for variant detection with GATK on Iontorrent PGM/Proton data?

Any plans for GATK branches to deal with the particulars of IonTorrent output?

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Hi,

I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK?

Thanks, XZ

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I am trying to merge two vcfs (SNVs and INDELs) from the same sample. The problem appears to be that the INDEL vcf defines "combined_sample_name" but the SNV vcf does not. So when I merge I get two sample columns. How can I force GATK to treat them as a single sample?

I tried --assumeIdenticalSamples to do a "simple merge," but that made no difference.

As a side note, these vcfs are from an Ion Torrent machine.

Thanks!

java -jar $GATK \
    -R $TSP_FILEPATH_GENOME_FASTA \
    -T CombineVariants \
    --assumeIdenticalSamples \
    -V:${baseFolderName} ${i}/SNP_variants.vcf \
    -V:${baseFolderName} ${i}/indel_variants.vcf \
    -o ${RESULTS_DIR}/${baseFolderName}_variants.vcf

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