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 fist time for a 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 mergin...
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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 combine gVCFs and genotype call) in IGV. I see SNPs that are just only in one of the samples in eit...
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Alia Parveen commented,
I also have 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 latest reference genome using BWA and generated .sam, .ba...