Laura Rey Vargas
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Activity overview
Latest activity by Laura Rey Vargas-
Laura Rey Vargas created a post,
Seeking Clarification on RNA-seq Variant Calling Pipeline
I am currently working on variant calling from RNA-seq data and have encountered some discrepancies between the pipeline I am using and the one recommended by GATK. I am reaching out to seek clarif...
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Laura Rey Vargas commented,
Thank you so much for the help. I will implement this new step as you suggested.
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Laura Rey Vargas commented,
i checked the bam files and they do have information. I obtained read counts from them and also ran various quality metrics and they seem good. Maybe it is something else
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Laura Rey Vargas commented,
I did not check the bam files, but I will now. To generate the GVCF files i followed these steps: 1. Alignment with STAR: STAR_options="--runThreadN 20 \--limitGenomeGenerateRAM 100000000000 \--ge...
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Laura Rey Vargas commented,
As far as I checked, HaplotypeCaller did not present any errors. I ran the command line you suggested in only one of the samples, and this is what I got: chr1 1 . N <NON_REF> ...
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Laura Rey Vargas commented,
Thank you for the response, however, your suggestions did not work. I tried running GenotypeGVCFs with only one of the vcf files I got from the HaplotypeCaller, instead of the input gendb://my_data...
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Laura Rey Vargas created a post,
GenotypeGVCFs generates an empty VCF file with all my samples
REQUIRED for all errors and issues: a) GATK version used: v4.2.2.0b) Exact command used: output_dir="/home/wovalle3/LREY/variant_call/prueba" gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport...