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3.1 years ago
Alewa
▴
150
I'm working with a tool that accepts only ICGC-like mutation formats. https://docs.icgc.org/submission/guide/icgc-simple-somatic-mutation-format/
Any suggestions / tools to convert my normal vcf file (i meant like this https://samtools.github.io/hts-specs/VCFv4.2.pdf) to ICGC-like VCFs?
Thanks in advance
I have attached example of my vcf (without headers)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SC173874 SC173909
chr1 35816826 . G A . PASS ALIGN_DIFF=63;AS_FilterStatus=SITE;AS_SB_TABLE=57,27|3,1;DP=95;ECNT=1;FUNCOTATION=[AGO4|hg38|chr1|35816826|35816826|INTRON||SNP|G|G|A|g.chr1:35816826G>A|ENST00000373210.3|+|||c.e2-56G>A|||0.42643391521197005|AAAAAAGAAAGAAAGAAAGAA|||||||||||||||||||||||||||||CH471059|NM_017629.3|NP_060099|HGNC:18424|argonaute_%20_4_%2C__%20_RISC_%20_catalytic_%20_component|Approved|gene_%20_with_%20_protein_%20_product|protein-coding_%20_gene|EIF2C4|"eukaryotic_%20_translation_%20_initiation_%20_factor_%20_2C_%2C__%20_4"_%2C__%20_"argonaute_%20_RISC_%20_catalytic_%20_component_%20_4"|hAGO4_%2C__%20_KIAA1567_%2C__%20_FLJ20033|"argonaute_%20_4"|1p34.3|2016-10-05|2013-02-15|2015-11-27|AB046787||192670|ENSG00000134698|12906857|NM_017629|408|Argonaute/PIWI_%20_family|CCDS397|OTTHUMG00000004243|192670|607356|NM_017629|Q9HCK5|ENSG00000134698|uc001bzj.3||||AGO4_HUMAN||A7MD27|Q9HCK5|epidermal_%20_growth_%20_factor_%20_receptor_%20_signaling_%20_pathway_%20_(GO:0007173)_%7C_Fc-epsilon_%20_receptor_%20_signaling_%20_pathway_%20_(GO:0038095)_%7C_fibroblast_%20_growth_%20_factor_%20_receptor_%20_signaling_%20_pathway_%20_(GO:0008543)_%7C_gene_%20_expression_%20_(GO:0010467)_%7C_innate_%20_immune_%20_response_%20_(GO:0045087)_%7C_mRNA_%20_catabolic_%20_process_%20_(GO:0006402)_%7C_negative_%20_regulation_%20_of_%20_translation_%20_involved_%20_in_%20_gene_%20_silencing_%20_by_%20_miRNA_%20_(GO:0035278)_%7C_neurotrophin_%20_TRK_%20_receptor_%20_signaling_%20_pathway_%20_(GO:0048011)_%7C_Notch_%20_signaling_%20_pathway_%20_(GO:0007219)_%7C_phosphatidylinositol-mediated_%20_signaling_%20_(GO:0048015)|cytoplasmic_%20_mRNA_%20_processing_%20_body_%20_(GO:0000932)_%7C_cytosol_%20_(GO:0005829)_%7C_membrane_%20_(GO:0016020)_%7C_micro-ribonucleoprotein_%20_complex_%20_(GO:0035068)_%7C_RISC_%20_complex_%20_(GO:0016442)|miRNA_%20_binding_%20_(GO:0035198)|||||||||||||||||||false|false||false|false||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false||||||||||||||||||||||||||||||||||||||||||||3.60985e-04|5.05433e-04|5.98086e-04|4.37637e-04|0.00000e+00|0.00000e+00|0.00000e+00|3.81679e-03|0.00000e+00|5.15464e-03|0.00000e+00|0.00000e+00|0.00000e+00|3.28192e-04|4.04531e-04|7.66871e-04|0.00000e+00|3.86747e-04|2.88060e-04|0.00000e+00|1.63666e-04|3.85802e-04|2.48942e-04|5.29101e-04|1.61290e-02|0.00000e+00|0.00000e+00|0.00000e+00|5.05433e-04|1.55971e-03||1|36282427|false|false|rs1296156478|RF|SC173909|SC173874|Unknown|CRC_PR];GERMQ=93;MBQ=30,20;MFRL=233,315;MMQ=60,50;MPOS=27;NALIGNS=53;NALOD=1.21;NLOD=12.72;POPAF=2.71;ROQ=12;TLOD=6.51;UNITIGS=124 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:36,4:0.109:40:9,0:21,4:26,10,3,1 0/0:48,0:0.021:48:23,0:23,0:31,17,0,0
chr1 48471987 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=61,82|3,2;DP=155;ECNT=1;FUNCOTATION=[SPATA6|hg38|chr1|48471987|48471987|MISSENSE||SNP|G|G|T|g.chr1:48471987G>T|ENST00000371847.7|-|1|187|c.22C>A|c.(22-24)Cag>Aag|p.Q8K|0.71571072319202|AGGGCGCACTGCAGCGCCTTC|SPATA6_ENST00000371843.7_MISSENSE_p.Q8K/SPATA6_ENST00000396199.7_MISSENSE_p.Q8K||||||||||||||||||||91|biliary_tract(2)_%7C_breast(12)_%7C_central_nervous_system(44)_%7C_large_intestine(11)_%7C_pancreas(22)|||||||HM005491|NM_019073.3|NP_061946|HGNC:18309|spermatogenesis_%20_associated_%20_6|Approved|gene_%20_with_%20_protein_%20_product|protein-coding_%20_gene|||SRF1_%2C__%20_FLJ10007_%2C__%20_SRF-1|"spermatogenesis-related_%20_factor-1"|1p33|2016-10-05|||AK000869||54558|ENSG00000132122||NM_019073|||CCDS551_%2C__%20_CCDS65535_%2C__%20_CCDS72787|OTTHUMG00000007794|54558|613947|NM_001286238|Q9NWH7|ENSG00000132122|uc001crr.4||||SPAT6_HUMAN||Q5T3N7_%7C_Q8WUE6|Q9NWH7|cell_%20_differentiation_%20_(GO:0030154)_%7C_multicellular_%20_organismal_%20_development_%20_(GO:0007275)_%7C_spermatogenesis_%20_(GO:0007283)|extracellular_%20_region_%20_(GO:0005576)||||||||||||||||||||false|false||false|false||false|false|false||false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|false|||false|false||false||false||false|false|false||false|||false|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||false|false|||SC173909|SC173874|Unknown|CRC_PR];GERMQ=93;MBQ=30,20;MFRL=248,175;MMQ=60,60;MPOS=60;NALIGNS=1;NALOD=1.89;NLOD=22.87;POPAF=6.00;ROQ=24;TLOD=7.51;UNITIGS=205 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:51,5:0.087:56:27,3:24,2:23,28,3,2 0/0:92,0:0.013:92:36,0:56,0:38,54,0,0
