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nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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Add genomic coordinates for Dave's KIR-2DL1 gene features #101

Closed ckennedy-nmdp closed 9 years ago

ckennedy-nmdp commented 9 years ago

--> testing whether the current pipeline will filter pre-assembled KIR

ckennedy-nmdp commented 9 years ago

Using ngs-filter-consensus with tutorial/regions/grch38/kir/kir-2dl1.exons.txt and translating the resulting cDNA results in the correct amino acid sequence: MSLLFVSMACVGFFLLQGAWPHEGVHRKPSLLAHPGPLVKSEETVILQCWSDVMFEHFLL HREGMFNDTLRLIGEHHDGVSKANFSISRMTQDLAGTYRCYGSVTHSPYQVSAPSDPLDI VIIGLYEKPSLSAQPGPTVLAGENVTLSCSSRSSYDMYHLSREGEAHERRLPAGPKVNGT FQADFPLGPATHGGTYRCFGSFHDSPYEWSKSSDPLLVSVTGNPSNSWPSPTEPSSKTGN PRHLHILIGTSVVIILFILLFFLLHRWCSNKKNAAVMDQESAGNRTANSEDSDEQDPQEV TYTQLNHCVFTQRKITRPSQRPKTPPTDIIVYTELPNAESRSKVVSCP-

ckennedy-nmdp commented 9 years ago

Nope, not right. Had to fix a hardcoded reference name in FilterConsensusSequence (see ngs/ repo pull request) and change some test and tutorial files.