Alia Parveen
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Activity overview
Latest activity by Alia Parveen-
Alia Parveen created a post,
Too many variants after WGS workflow for a pig line
I used GATK for the very first time for whole genome sequencing data in a pig line. I am seeing way too many SNPs and INDELS. I used Haplotype Caller to generate gVCF files and Combine for merging...
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Alia Parveen commented,
Thank you and it worked. I have one more question. I see way too many SNPs in my final vcf (after the genotype call) in IGV. I see SNPs that are only in one of the samples in either case or control...
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Alia Parveen commented,
I also encountered the same error and my sorted bam files do not have @RG lines. I was given trimmed fastq files (2 years old) that I aligned with the latest reference genome using BWA and generate...