# HG changeset patch # User sanbi-uwc # Date 1534419663 14400 # Node ID fc75be7f3fd24716ceb3a11ddc76130c27eb8354 planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit a7c330a5dff63e78b9ff963a0b380937d27f4449 diff -r 000000000000 -r fc75be7f3fd2 intersect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/intersect.xml Thu Aug 16 07:41:03 2018 -0400 @@ -0,0 +1,69 @@ + + + Intersect SNPs with a CSV file + + vcf_snps_utils_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated) + +Usage: vcf_snps_utils intersect [OPTIONS] [VCFFILES]... CSVFILE + +----- + +**Example** + + VCF snp intersect tool (CSV file). + + This tools compares CSV snps to the VCF snps This is to establish whether + the discovered (VCF snps) have been discovered in the pass. This will + potential be extended to include verification using other external source + such as databases/api. + + CSV File passed should be in the following format (Example): + position in H37Rv gene short name snp_type Reference Sample1 Sample2 Sample3 + 1285 dnaA dnaA1285 nsSNP G G G G + 4013 recF recF4013 nsSNP T C C C + + Report bugs to: combattb-help@sanbi.ac.za CombatTB home page: + General help using CombatTB + software: + +Options: + --out TEXT set the output directory, default is + "/tmp/vcf_snps_utils_output/" + --help Show this message and exit. + + vcf_snps_utils intersect example.vcf example.csv --out output/test + + + + diff -r 000000000000 -r fc75be7f3fd2 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Thu Aug 16 07:41:03 2018 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 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