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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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ERROR: Invalid character (2) found! #22

Open wqy399 opened 4 years ago

wqy399 commented 4 years ago

Hello! When I ran RAiSD with the following command line: raisd-master/RAiSD -n my -I /data/select/pop/test1.vcf ，I got this error: ERROR: Invalid character (2) found! It seemed that something was wrong with my vcf file. It contains 1 chromosome. Actually I generatede the vcf file for 9 individuals with GATK4, then separated them to different chromosomes. Here is a part of my vcf : 1 1964 HiC_scaffold_1_1964 A G 246.57 . AC=5;AF=0.500;AN=10;BaseQRankSum=0.842;DP=27;ExcessHet=3.5218;FS=6.761;MLEAC=7;MLEAF=0.7 00;MQ=25.68;MQRankSum=0.00;QD=10.27;ReadPosRankSum=0.00;SOR=2.252 GT:AD:DP :GQ:PL 0/1:3,4:7:54:100,0,54 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0
./.:1,0:1:.:0,0,0 0/0:1,0:1:3:0,3,30 1/1:0,3:3:9:89,9,0 ./.:0,0: 0:.:0,0,0 0/1:4,2:6:33:33,0,83 0/1:6,2:8:27:27,0,150 Could you please tell me what was wrong ? Thanks a lot!

alachins commented 4 years ago

There is an invalid character in your dataset, but it's not in the vcf part you include in your post. I can look into your vcf file to point out what's wrong. Also, you do not need to separate the chromosomes. RAiSD will detect that and separate them internally.

wqy399 commented 4 years ago

Thanks for your reply! I think I have solved this problem and I guess the issue was I modified the items in columns of "CHROM" and "ID" in vcf file, for example from "HiC_scaffold_1" to "1" with "awk" command. When I used the initial version, RAiSD ran normally.