search

bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
994 stars 354 forks source link

varscan vcf #493

Closed kspham closed 10 years ago

kspham commented 10 years ago

It seems that the output VCF from varscan in bcbio-nextgen can not be used further for VarScan.jar somaticFilter?

java -jar /usr/local/share/java/varscan/VarScan.v2.3.6.jar somaticFilter 2your-arbitrary-batch-name.vcf --output-file myoutput.vcf Parsing Exception on line: 1 10146 rs375931351 AC A 0 PASS AC=2;AF=0.500;AN=4;DP=479;GC=50.50;GPV=4.6009E-42;HRun=4;MQ=12.79;SPV=7.0606E-1;SS=1;SSC=1;DB GT:AD:DP:DP4:FREQ:RD 0/1:71:475:252,148,23,48:0.1507:400 0/1:59:426:233,129,27,32:0.1401:362 For input string: "252,148,23,48" Parsing Exception on line: 1 10177 . A AC 0 PASS AC=2;AF=0.500;AN=4;DP=478;GC=50.50;GPV=2.0125E-34;HRun=0;MQ=10.85;SPV=9.7791E-1;SS=1;SSC=0 GT:AD:DP:DP4:FREQ:RD 0/1:59:171:38,41,41,18:0.4275:79 0/1:37:142:36,45,25,12:0.3136:81 1 10230 rs376846324 AC A 0 PASS AC=2;AF=0.500;AN=4;DP=462;GC=48.51;GPV=1.0816E-16;HRun=4;MQ=16.28;SPV=1.2965E-1;SS=1;SSC=8;DB GT:AD:DP:DP4:FREQ:RD 0/1:21:165:63,75,5,16:0.1321:138 0/1:29:160:61,67,10,19:0.1847:128 For input string: "63,75,5,16" Parsing Exception on line: 1 10250 rs199706086 A C 0 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=1.183;DP=359;FS=10.594;GC=51.49;GPV=1.2812E-9;HRun=3;HaplotypeScore=118.6974;MQ=18.29;MQ0=142;MQRankSum=-1.627;ReadPosRankSum=0.525;SPV=9.0224E-1;SS=1;SSC=0;DB GT:AD:DP:DP4:FREQ:RD 0/1:137,33:93:30,45,7,9:0.1758:75 0/1:153,21:102:22,66,8,4:0.12:88 For input string: "30,45,7,9" Too many parsing exceptions encountered; exiting

chapmanb commented 10 years ago

Son; As far as I can tell, VarScan's somaticFilter either does not support VCF input or has incomplete support for VCF input:

http://sourceforge.net/p/varscan/discussion/1073559/thread/f95f0072/

We've not been exploring integration with VarScan downstream since the original variant calls haven't been as sensitive as other methods. Do you specifically need somaticFilter, or does the filtering done by bcbio from scratch work for you?