Hi all,
I'm trying to use CoNIFER on some exome data (Illumina TruSeq enrichment) and I could successfully use the whole package. Nevertheless I have at least one sample previously validated which cannot be called. Values for exported ZRPKM for the validated gene are reported below. As you can see there's a deletion at the end of the gene (Z < -2). When I run confier call this region is not listed, although I'm using default threshold of 1.5. Can anybody help to spot what's happening here?
Thanks
d
Hi all,
I'm trying to use CoNIFER on some exome data (Illumina TruSeq enrichment) and I could successfully use the whole package. Nevertheless I have at least one sample previously validated which cannot be called. Values for exported ZRPKM for the validated gene are reported below. As you can see there's a deletion at the end of the gene (Z < -2). When I run confier call this region is not listed, although I'm using default threshold of 1.5. Can anybody help to spot what's happening here?
Thanks
d
chr16 2325878 2326806 ABCA3 1.799780
chr16 2327597 2327671 ABCA3 1.228749
chr16 2327879 2328070 ABCA3 0.116366
chr16 2328288 2328459 ABCA3 -0.930164
chr16 2328943 2329131 ABCA3 0.071382
chr16 2331027 2331222 ABCA3 -0.396744
chr16 2331381 2331510 ABCA3 -0.390571
chr16 2333186 2333359 ABCA3 -0.199653
chr16 2334279 2334438 ABCA3 -0.588328
chr16 2334779 2334999 ABCA3 0.372528
chr16 2335442 2335647 ABCA3 0.030888
chr16 2336694 2336968 ABCA3 0.698320
chr16 2338026 2338330 ABCA3 0.899572
chr16 2339434 2339621 ABCA3 -0.074022
chr16 2342140 2342239 ABCA3 0.735194
chr16 2345590 2345741 ABCA3 -0.050358
chr16 2347329 2347540 ABCA3 -0.150348
chr16 2347766 2347922 ABCA3 1.248490
chr16 2348386 2348541 ABCA3 0.502709
chr16 2349403 2349533 ABCA3 -1.208224
chr16 2350005 2350149 ABCA3 0.331823
chr16 2353969 2354151 ABCA3 0.046606
chr16 2358450 2358624 ABCA3 -0.121586
chr16 2367283 2367404 ABCA3 0.592293
chr16 2367648 2367765 ABCA3 0.697754
chr16 2369581 2369841 ABCA3 0.434000
chr16 2373523 2373689 ABCA3 0.219927
chr16 2374404 2374532 ABCA3 -2.934594
chr16 2376010 2376275 ABCA3 -2.263931
chr16 2376413 2376493 ABCA3 -2.305526
chr16 2378453 2378758 ABCA3 -2.422985
chr16 2390573 2390747 ABCA3 -0.209644
/*
Davide Cittaro, PhD
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Center for Translational Genomics and Bioinformatics
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