Hi everyone, I am very new to STAR alignment and confused about the difference between total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab). …

Hi, everyone! I am new to the gatk pipelines, so I'm not sure is it necessary to use the -M option in the bwa men …

hi i work on samples that i have to find a meaningful snp in the section of baserecalibrator of gatk our output is .table my …

Hi everyone, I knew that there is a big difference between Polygenic risk scores (PRS) and haplotype. However, for me, they are likely the same …

Hi, I am counting variants using gatk HaplotypeCaller, however, I am not sure the difference between two options, MappingQualityReadFilter and MappingQualityFilter. I read the documents, …

Hi all! I would like to ask what is the scale of genotype quality? I've red that GATK still annotate variants with GQ 1-99. I …

Hello Everyone, I was trying freebayes on a small bam file and wanted to compare the quality of its output -vcf1- against the quality of …

For eqtl analysis, I used mach admix to imputed SNP6 array data against 1000G. Then the next step which got me confused is which SNP …

hi everyone I use GATK to do snp call. But I don't understand the BaseRecalibration report as follows . And I really don't known the …

Hi everyone, I use GATK to do SNP call.But the BaseRecalibration report confused me. what is reported quality scores and the empirical quality. what is …