
danilovkiri
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Votes on activity by danilovkiri Sort by votes-
LG Shortly, it is better to do. There is no strict rule and I will not provide you with one. Mind your sequencing provider.
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Hi! You can use FastqQC only as a general tool to assess the quality of obtained fastq data including adapter sequences. The FastQC adapter sequences search is implemented using specific Kmers defi...
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Hi Linda Do Such simple tasks do not require such complex solutions. There is a BCFtools package for any manipulations with VCF files. All you have to do is to run bcftools view -O v -o <output_vcf...
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Does anyone around you have Linux/macOS? It is really the easiest way since Windows is not supported by definitely all the bioinformatics tools (it not because the developers are Linux fans, howeve...
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Hi Damian Loska No, you will not have any problems. The Verily's build is described here (https://cloud.google.com/life-sciences/docs/resources/public-datasets/reference-genomes) with all the diffe...
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Hi DHWANI DHOLAKIA It is necessary to read ALL the documentation prior to using the tool. GenotypeGVCFs has a very unambiguous argument --include-non-variant-sites which is explicitly stated at htt...
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Cecilia Kardum Hjort Please look at your very initial query in this thread and describe how you solved the problem. You were talking about SortVCF, not MergeVCFs. Please elaborate so that other use...
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DHWANI DHOLAKIA UnifiedGenotyper documentation is also available at the link in my previous comment. The exact file is here (https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-tooldocs/3...
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Yes, GATK3.8 supports ERC modes in the exact same manner, the documentation (archived) can be found at https://github.com/broadinstitute/gatk-docs/tree/master/gatk3-tooldocs/3.8-0 The file you are ...
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Hi Lucas Kopecky Bobadilla The fact that the uBAM is readname-sorted and the mapped BAM is coordinate-sorted is the exact problem causing the error you are reporting. Both uBAM and mapped BAM must ...