I managed to compare the vcf files between two samples using vcftools perl script. However, I got the error messages in the following. It seems to do with the index file. What does it mean? Does this mean the index file is not in the correct format or anything I did it in a wrong way?
Your help is greatly appreciated
compare-vcf 441_M1_1x_SNP.vcf 441_2x_SNP.vcf
[main] fail to load the index file.
The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error. Is the file tabix indexed?
at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 422
Vcf::throw('Vcf4_0=HASH(0x9764fc8)', 'The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error...') called at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 1547
Vcf::get_chromosomes('Vcf4_0=HASH(0x9764fc8)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 100
main::compare_vcfs('HASH(0x961c818)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 12
weiyu@weiyu-VIG555M:~/test_for_vcf_snp$ tabix -l 441_M1_1x_SNP.vcf
[main] fail to load the index file.
Your help is greatly appreciated
compare-vcf 441_M1_1x_SNP.vcf 441_2x_SNP.vcf
[main] fail to load the index file.
The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error. Is the file tabix indexed?
at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 422
Vcf::throw('Vcf4_0=HASH(0x9764fc8)', 'The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error...') called at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 1547
Vcf::get_chromosomes('Vcf4_0=HASH(0x9764fc8)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 100
main::compare_vcfs('HASH(0x961c818)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 12
weiyu@weiyu-VIG555M:~/test_for_vcf_snp$ tabix -l 441_M1_1x_SNP.vcf
[main] fail to load the index file.
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