Entering edit mode
11.0 years ago
biokaervas
•
0
I'm sorry about this caotic question, but I don't understand nothing at all...
I have a file of Indels finded in genes, presumably from HGMD. Well, i don't know how to read this file, i don't have any headers that explains the different columns.
An extract from a file:
646 646 CCDS759.1 646 VS/S chr1|100346671|GTTT/T
1312 1314 CCDS778.1 1311 GFPG/G chr1|103379941|TCCAGGAAAA/A
920 925 CCDS778.1 919 PQGPQGP/P chr1|103440416|TGGACCCTGAGGTCCTTGA/A
270 270 CCDS803.1 269 KK/K chr1|110146634|CTTC/C
367 371 CCDS142.1 367 LCRQDR/R chr1|12023594|TGTGCCGGCAGGACCG/G
531 531 CCDS142.1 531 EK/K chr1|12026317|GAGA/A
378 380 CCDS30587.1 377 SLHM/S chr1|12062134|CCTGCACATG/G
706 708 CCDS30587.1 706 RENL/L chr1|12069699|GGGAGAACCT/T
584 584 CCDS1071.1 583 SS/S chr1|154570909|GATG/G
503 503 CCDS1102.1 502 SS/S chr1|155204885|AGAG/G
482 488 CCDS1102.1 482 LDAVALM/W chr1|155205025|ATCAGTGCCACTGCGTCCAG/CA
426 426 CCDS1102.1 426 EG/G chr1|155205578|CTTC/C
101 101 CCDS1102.1 100 GT/G chr1|155209679|GTGC/C
85 85 CCDS1102.1 84 GR/G chr1|155209727|CGCC/C
74 74 CCDS1102.1 73 GT/G chr1|155209760|GTAC/C
111 112 CCDS14215.1X 111 A/AA chrX|25031777|G/GCCG
111 112 CCDS14215.1X 111 A/AAA chrX|25031777|G/GCCGCCG
111 112 CCDS14215.1X 111 A/AAAA chrX|25031777|G/GCCGCCGCCG
426 427 CCDS14223.1X 426 I/II chrX|30322828|G/GATG
21 23 CCDS14231.1X 21 EL/VFYQNDS chrX|31279085|GAGCT/ACTGTCATTTTGGTAAAAGA
186 187 CCDS14242.1X 186 I/ILI chrX|37655281|A/CCTCATA
193 194 CCDS14242.1X 193 T/TSST chrX|37655302|C/TTCCTCCACC
195 196 CCDS14242.1X 196 I/KTI chrX|37655310|T/AAACCAT
388 390 CCDS14242.1X 388 GP/VFS chrX|37664273|GGCC/TGTTCAG
506 509 CCDS14242.1X 506 QKT/HIWA chrX|37668879|AAAGA/CATCTGGG
I figure out that first parragraph are deletions, and second insertions, and that's all...
I would like also, covert this strange notation into hgvs notation, at protein level.
Anyone knows how to deal with this?
Carlos.
