a5c144db4d
added scripts to generate hs38a.fa and hs38d6.fa
2014-11-13 12:53:29 -05:00
fffe52a45b
move bwa-typeHLA back to this repo
2014-11-13 12:50:56 -05:00
904afefbc6
r985: fix bug due to the lack of _pri contigs d6
2014-11-13 12:12:41 -05:00
c5fe18438a
r984: updated to the latest kseq.h
2014-11-13 11:12:23 -05:00
7eabcf42c4
r983: bugfix - wrong mate info
...
Picard now gives a clean bill.
2014-11-10 13:15:11 -05:00
a81603217e
mate chr is sometimes wrong
2014-11-10 10:16:53 -05:00
b2b42cea7e
removed contig weight & code cleanup
...
Contig weight was calculated based on a false assumption. It is actually not useful.
2014-11-07 12:45:01 -05:00
4e97cdfde8
move to a new project bwa-typeHLA
...
The two scripts cannot be used standalone anyway.
2014-11-06 09:13:15 -05:00
c2f2cb03ce
to be moved to a separate project
2014-11-06 09:12:53 -05:00
1bee29ef44
map to individual HLA ALT for meaningful mapQ
2014-11-06 00:37:59 -05:00
10de1e0b74
optionally output debegging info
2014-11-05 13:20:33 -05:00
0eee4fa1b0
nothing, really
2014-11-04 16:00:25 -05:00
2a41772d0a
more command line help
2014-11-04 15:41:18 -05:00
e5d7f4fc30
change the default max_len
2014-11-04 15:31:33 -05:00
ccf03ffd22
control min-match-length
...
we still need this to kill false mapping/alignment
2014-11-04 15:26:10 -05:00
de268247db
type primary exons first and then the rest
2014-11-04 15:09:21 -05:00
12fff1ad57
a bit code cleanup
2014-11-04 14:30:31 -05:00
96fba0f2f4
proper homozygous typing; fixed a low-level bug
2014-11-04 11:38:05 -05:00
ace18171b0
backup
2014-11-04 10:07:14 -05:00
4cbb0cb829
polished the run script
2014-11-03 15:29:02 -05:00
9dbf152e31
added the pipeline script
2014-11-03 15:16:14 -05:00
40c4a6ffe1
better CLI; more comments
2014-11-03 12:09:29 -05:00
4bc01e90c8
not used any more
2014-11-03 11:51:25 -05:00
b7d0a2d537
first HLA typing script
2014-11-03 11:47:23 -05:00
9bf898fa10
r963: expose mask_level
2014-10-30 11:33:43 -04:00
6db2fd98aa
r960: merge changes from the master branch
2014-10-28 13:46:40 -04:00
0f8a164bd3
bugfix: .ctw not generated properly
2014-10-25 23:08:29 -04:00
2bfcc421d9
bugfix: alignments not outputted
2014-10-25 22:13:31 -04:00
7327f8fa10
output all overlapping HLA hits
...
A contig longer than HLA genes may not get hits to HLA and thus won't be used
in typing.
2014-10-25 12:00:15 -04:00
33938e1ed0
save reads mapped to each HLA gene
...
for downstream typing
2014-10-24 16:54:48 -04:00
ba3ab0ca98
removed hla typing - not good enough
2014-10-24 14:52:16 -04:00
7a8019e6ee
removed debugging code
2014-10-24 14:51:05 -04:00
7c362bef69
added another paper
2014-10-23 15:15:20 -04:00
3a1da27c1c
added Bai et al. Seems good, too.
2014-10-23 15:08:18 -04:00
d61a1226a8
highlight Liu et al. It seems good.
2014-10-23 14:52:48 -04:00
f005ea4bf3
coarse HLA typing and doc
2014-10-23 14:42:45 -04:00
3d129be642
r943: change the default -y to 20, but ...
...
for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy
because a locus at chr19 has 35 copies.
2014-10-22 12:42:58 -04:00
4177d6c2c7
r942: ignore ALT hits when counting n_sub for ...
...
non-ALT hits. Counting leads to underestimated mapQ.
2014-10-22 10:24:16 -04:00
60b728487a
r941: set a min length for 3rd-round seeding
2014-10-21 13:15:42 -04:00
282130a64e
r940: fixed a bug - missing primary hit
2014-10-21 12:57:49 -04:00
5e00d08346
r939: fixed a memory leak (issue #35 )
2014-10-21 09:26:19 -04:00
574098d034
updated directory name
2014-10-21 00:57:06 -04:00
4260699a09
updated ALT readme due to recent changes
2014-10-21 00:55:00 -04:00
76a15ea91b
r933: with bwa-postalt ready, drop option -g
2014-10-21 00:23:14 -04:00
2bfa3c767b
CLI help
2014-10-21 00:22:59 -04:00
497913d404
working largely as expected
2014-10-21 00:16:41 -04:00
a6b5a30dab
r930: use 3rd round seeding by default
...
This strategy is similar to the seeding heuristic used by LAST. When it is used
alone, it is not as accurate as the current seeding strategy at least for short
reads. However, it may do a better job for a long contig mapped to multiple ALT
contigs. This seeding strategy is also relatively cheap to perform.
2014-10-20 17:34:15 -04:00
038af2a551
r929: added simplified LAST-like seeding
2014-10-20 17:00:31 -04:00
25d45512d9
code backup
2014-10-20 14:17:56 -04:00
6f41a27e27
towards adding "-r" to postprocessing
2014-10-19 20:53:47 -04:00
Heng Li