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Where can I find dbsnp_144.hg38.vcf.gz
I'm installing an application that uses files from the GATK resource bundle. I found all of the needed files at...
View ArticleAre there issues with using reads coming from different technologies and...
Hello! We are analyzing a WGS data of 60 samples (6 groups, 10 samples/group) produced by HiSeq4000. The mean coverage per sample is 25x (lowest sample is 15x). Now we realized we need to sequence more...
View ArticleHow to add sample names in VCF?
I am using GATK best practices for germline SNPs and Indels 4.1.2.0. After mapping and recalibration, I run haplotypecaller in GVCF mode. I am combining all vcf files (output from haplotypecaller)...
View ArticleMissing PS field in the VCF file produced by GenotypeGVCFs
Hello, I followed GATK best practices to produce a VCF file for 20 individuals. GATK version is 4.1.0.0. The BAM files were all verified by ValidateSamFile, no errors or warnings were detected....
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