Heather Tuttle
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Activity overview
Latest activity by Heather Tuttle-
Heather Tuttle commented,
I will request to update to the newest version of GATK from the supercomputing institute that I work with. Until then, I will try using the flag and give an update! Thanks!
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Heather Tuttle commented,
That really doesn't help me at all. It does not tell me why MQ scores are missing or why they are not being transferred to the VCF from the bam. The scores are all present in the bams! I have run...
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Heather Tuttle commented,
MQ is also not in the VCF, whereas everything else is. I noticed that I was using haplotypecaller 4.1.2 and then using combineGVCF and GenotypeGVCF 4.0.6. Could this be the issue?
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Heather Tuttle commented,
I have tried recalling haplotypes with -A RMSMappingQuality and going through the pipeline again, and still no MQ. MQ is a standard annotation usually, right? I am able to get every other annota...
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Heather Tuttle commented,
You can find published datasets at pubmed (NCBI). You need to familiarize yourself with this site first!
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Heather Tuttle created a post,
Missing MQ scores in gvcf
Hello, I am trying to hard filter my vcf and I am using: module load gatk/4.0.6 gatk VariantsToTable -V diploid_genotyped_v102220.g.vcf -F MQ -O diploid_genotyped_unfiltMQ_v102220.txt The resul...