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ding-lab / CharGer

Characterization of Germline variants
https://ding-lab.github.io/CharGer/
GNU General Public License v3.0
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can't input maf.file #30

Closed rescuz closed 5 years ago

rescuz commented 5 years ago

Hello, When I input maf.file ，charger always print "CharGer Error: bad .maf file ",so i want to know whether there are some errors in my maf.file .I paste my maf.file content in follow,many thanks!

maf.file: 1 Hugo_Symbol Entrez_Gene_Id Chromosome Start_position End_position Variant_Classification Variant_Type Reference_Allele Tumor 2 CDK11A 728642 1 1647893 1647894 In_Frame_Ins INS - - TTTCTT rs200224067|rs199866927|rs144636354 3 PRDM2 7799 1 14106394 14106395 In_Frame_Ins INS - - CTC rs2308040|rs148293494|rs59028030
4 SLC25A34 284723 1 16063253 16063265 Frame_Shift_Del DEL CAGCCTGGCGTGC CAGCCTGGCGTGC - BGI-0 5 SERINC2 347735 1 31905889 31905890 In_Frame_Ins INS - - CAG rs33956499|rs3050461|rs5773362 byFrequency 6 GJB4 127534 1 35227008 35227011 Frame_Shift_Del DEL TGTC TGTC - rs146812843 BGI-0103-ESCC-060N 7 MAP7D1 55700 1 36643701 36643703 In_Frame_Del DEL AGA AGA - rs3045695|rs141305015|rs200892098 byFre 8 KLF17 128209 1 44596380 44596382 In_Frame_Del DEL CAA CAA - rs200059598|rs34057178 byFrequency 9 CYP4B1 1580 1 47280747 47280748 Splice_Site DEL AT AT - rs55835239|rs397687617|rs3215983

fernanda-rodrigues commented 5 years ago

Can you attach your maf file here so I can do some testing? The file you pasted here does not contain the HGVSc and HGVSp columns that CharGer looks for, causing it to issue the "CharGer Error: bad .maf file " error message.

fernanda-rodrigues commented 5 years ago

I am closing this issue. Please do not hesitate to contact us if you have further questions.

Fernanda