Melcar Collodetti
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Recent activity by Melcar Collodetti Sort by recent activity-
Our collaborators at the Intel-Broad Center for Genomic Data Engineering can provide you with recommended hardware configurations based on your planned usage. Let us know in the comment thread if y...
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You're welcome. Basically, what needs to be done is: -Fix the link to https://storage.googleapis.com/gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf -Index the raw file with: gatk-4.2...
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IT FINALLY WORKED: ./gatk-4.2.6.1/gatk GetPileupSummaries \ --disable-sequence-dictionary-validation true \ -I amostra1_sorted_rmdup_F4.bam \ -V af-only-gnomad.raw.sites.vcf.1 \ -...
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New try with GATK 4.2.2.0 and af-only-gnomad.raw.sites.vcf: gatk-4.2.2.0/gatk IndexFeatureFile -I af-only-gnomad.raw.sites.vcf after index was done: ./gatk-4.2.2.0/gatk GetPileupSummaries \ -...
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Changed GATK version to 4.2.6.1 and tried the following: ./gatk-4.2.6.1/gatk GetPileupSummaries \ --disable-sequence-dictionary-validation true \ -I amostra1_sorted_rmdup_F4.bam \ -V ...
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I also tried the rename step that Field-Ye-Tian suggested (https://gatk.broadinstitute.org/hc/en-us/community/posts/360073450391-A-USER-ERROR-has-occurred-af-only-gnomad-hg38-vcf-gz-because-no-suit...
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I also tried: wget https://storage.googleapis.com/gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf bgzip af-only-gnomad.raw.sites.vcf bcftools index -t af-only-gnomad.raw.sites.vcf.gz ...