Manuela Bonetto
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Activity overview
Latest activity by Manuela Bonetto-
Manuela Bonetto created a post,
Funcotator - WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:984456-984456 due to alternate allele: *
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: (I downloaded and untared the GATK pre-packeged data sources) $gatk Funcotator \-R $ref/uc...
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Manuela Bonetto created a post,
VQSR - indel MQ zero variance and
I'm having trouble with VariantRecalibrator on mode INDEL, don't really understand what's wrong... mode SNP ran smoothly with no errors. Can someone help?a) GATK version used: 4.1.8.1b) Exact comma...
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Manuela Bonetto commented,
Also, would like to add: HaplotypeCaller produced the g.vcf.gz's and g.vcf.gz.tbi's, all of these are in the same folder.
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Manuela Bonetto created a post,
Genomics DBImport - A USER ERROR has occurred: Failed to create reader from file:
I do not know what this error means. The file GATK4teste_cohort.sample_map.txt is in the following format: sample1 sample1.g.vcf.gz...samplen samplen.g.vcf.gz The file col1_mendelics_exoma_hg19.b...
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Manuela Bonetto created a post,
BaseRecalibrator - Failed to detect whether we are running on Google Compute Engine.and Input files reference and reads have incompatible contigs
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: java -jar $gatk BaseRecalibrator \--intervals $ref/mendelics_exoma_hg19.bed \-ip 100 \-I ...