When I apply the tabiz command: Tabix -p vcf file1.vcf.gz the following error appears: [ti_index_core] the file out of order at line 8. I had previous errors because I ...
t1 > > > > then bgzip and tabix, I got this error. > > ~/bin/tabix -s 1 -b 2 -e 3 genePosition.gz > > [ti_index_core] the file out of order at line 88 > ...
... 1_2014-02-18_tumor-paired-sort-chr7_6014222_55087104-prep-variants-10- 497--raw.vcf.gz [2014-03-07 10:47] [ti_index_core] the file out of order at lin...
... still shows up, could you give some suggestions? cat z.vcf | vcf-sort > out.vcf bgzip out.vcf tabix -p vcf out.vcf.gz. [ti_index_core] the file out of order at line 19.
[ti_index_core] the file out of order at line 176099 Error in value[[3L]](cond) : internal: samtools invoked 'exit(1)'; see warnings() and restart R file: ...
... name, parentenv, handler) : [ti_index_core] the file out of order at line 19. It seems my file is not in order, but what kind of order or how should ...
ti_index_core the file out of order ...
The '-l' option is not listed in the tabix manual document, but it is supposed to list the sequence names stored in the index of the bgzipped vcf file ...
Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file
-O, null, The combined GVCF output file. --reference -R, null, Reference sequence file. --variant -V, [], One or more VCF files containing variants.