From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
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"From FastQ Data to High‐Confidence ..." refers methods in this paper
...This is the u-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases versus those with the alternate allele)....
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...The u-based z-approximation from the Mann-Whitney Rank Sum Test (Mann and Whitney, 1947) for mapping qualities (reads with ref bases versus those with the alternate allele)....
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...This is the u-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele....
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...The u-based z-approximation from the Mann-Whitney Rank Sum Test (Mann and Whitney, 1947) for the distance from the end of the read for reads with the alternate allele....
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43,862 citations
29,504 citations
"From FastQ Data to High‐Confidence ..." refers methods in this paper
...RStudio IDE and the R libraries ggplot2 (Wickham, 2009) and gsalib (DePristo et al., 2011) 29....
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20,557 citations
"From FastQ Data to High‐Confidence ..." refers background in this paper
...Assembling and Mapping Large Sequence Sets 11.10.17 Current Protocols in Bioinformatics Supplement 43 Known and true sites training resource: Mills indel dataset (Mills et al., 2006) This resource is an indel call set that has been validated to a high degree of confidence....
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11,055 citations
"From FastQ Data to High‐Confidence ..." refers methods in this paper
...Genome Analysis Toolkit (GATK) (McKenna et al., 2010; DePristo et al., 2011) 24....
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...BWA (Li and Durbin, 2010) and GATK (McKenna et al., 2010; DePristo et al., 2011) are publicly available software packages that can be used to construct a variant-calling workflow following those principles....
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