; retrieve-variation-seq -v 2 -species Homo_sapiens -release 84 -assembly GRCh38 -i results/variation_scan_demo/variation_demo_set.varBed -mml 30 -format varBed -o results/variation_scan_demo/variation_demo_set.varseq ; Program version 1.18 ; Input files ; input results/variation_scan_demo/variation_demo_set.varBed ; Output files ; output results/variation_scan_demo/variation_demo_set.varseq ; Column contents ; 1 chr Chromosome ; 2 start Start position ; 3 end End position ; 4 strand Strand ; 5 id identifier ; 6 soterm Sequence ontology (SO) term describing variation type. ; 7 ref_var Reference variant ; 8 alt_var Alternative variant ; 9 allele_freq Frequency of the current allele ; 10 seq Sequence of the current variant, flanked by a user-specified neighbouring region #chr start end strand id soterm ref_var alt_var allele_freq seq 1 10108 10108 + rs62651026 SNV C T NA taaccctaaccctaaccctaaccctaaccTaaccctaaccctaaccctaaccctaaccc 1 10108 10108 + rs62651026 SNV C C NA taaccctaaccctaaccctaaccctaaccCaaccctaaccctaaccctaaccctaaccc 1 10150 10150 + rs371194064 SNV C T NA aaccctaaccctaaccctaaccctaacccTtaaccctaaccctaaccctaaccctaacc 1 10150 10150 + rs371194064 SNV C C NA aaccctaaccctaaccctaaccctaacccCtaaccctaaccctaaccctaaccctaacc 1 10228 10254 + rs200462216 deletion AACCCCTAACCCTAACCCTAAACCCTA NA aaccctaaccctaaccctaaccctaacccaaaccctaaccctaaccctaaccctaacc 1 10228 10254 + rs200462216 deletion AACCCCTAACCCTAACCCTAAACCCTA NA aaccctaaccctaaccctaaccctaacccaaaccctaaccctaaccctaaccctaacc 1 10228 10254 + rs200462216 deletion AACCCCTAACCCTAACCCTAAACCCTA AACCCCTAACCCTAACCCTAAACCCTA NA aaccctaaccctaaccctaaccctaacccAACCCCTAACCCTAACCCTAAACCCTAaaaccctaaccctaaccctaaccctaacc 1 14542 14542 + rs1045833 SNV A C NA gaagtccccgccccagctgtgtggcctcaCgccagccttccgctccttgaagctggtct 1 14542 14542 + rs1045833 SNV A T NA gaagtccccgccccagctgtgtggcctcaTgccagccttccgctccttgaagctggtct 1 14542 14542 + rs1045833 SNV A A NA gaagtccccgccccagctgtgtggcctcaAgccagccttccgctccttgaagctggtct 1 15817 15817 + rs2691316 SNV G A NA ccgctcaccttgctcctgctccttctgctActgcttctccagctttcgctccttcatgc 1 15817 15817 + rs2691316 SNV G C NA ccgctcaccttgctcctgctccttctgctCctgcttctccagctttcgctccttcatgc 1 15817 15817 + rs2691316 SNV G G NA ccgctcaccttgctcctgctccttctgctGctgcttctccagctttcgctccttcatgc 1 15820 15820 + rs2691315 SNV G A NA ctcaccttgctcctgctccttctgctgctActtctccagctttcgctccttcatgctgc 1 15820 15820 + rs2691315 SNV G C NA ctcaccttgctcctgctccttctgctgctCcttctccagctttcgctccttcatgctgc 1 15820 15820 + rs2691315 SNV G G NA ctcaccttgctcctgctccttctgctgctGcttctccagctttcgctccttcatgctgc 1 24832 24832 + rs452623 SNV A C NA ctcctctcgccgcaggtctggctggatgaCgggcacggcataggtctgacctgccaggg 1 24832 24832 + rs452623 SNV A T NA ctcctctcgccgcaggtctggctggatgaTgggcacggcataggtctgacctgccaggg 1 24832 24832 + rs452623 SNV A A NA ctcctctcgccgcaggtctggctggatgaAgggcacggcataggtctgacctgccaggg 1 13980 13980 + rs62635296 SNV T C 0.02066 gtcacctcccccaccttcttcctgagtcaCtcctgcagccttgctccctaacctgcccc 1 13980 13980 + rs62635296 SNV T T 0.02066 gtcacctcccccaccttcttcctgagtcaTtcctgcagccttgctccctaacctgcccc 1 94991 94991 + rs188832636 SNV G A 0.001377 tgagactacaggcacctaccaccacgcctAgctaatttttttttattttttatttttta 1 94991 94991 + rs188832636 SNV G G 0.001377 tgagactacaggcacctaccaccacgcctGgctaatttttttttattttttatttttta 1 30923 30923 + rs806731 SNV G A NA tttctctctatctcatttctctctctctcActatctcatttttctctctctctctttct 1 30923 30923 + rs806731 SNV G C NA tttctctctatctcatttctctctctctcCctatctcatttttctctctctctctttct 1 30923 30923 + rs806731 SNV G T NA tttctctctatctcatttctctctctctcTctatctcatttttctctctctctctttct 1 30923 30923 + rs806731 SNV G G NA tttctctctatctcatttctctctctctcGctatctcatttttctctctctctctttct ; Total variations 10 ; Total variants 27 ; Host name caminante.local ; Job started 2016-07-22.053618 ; Job done 2016-07-22.053626 ; Seconds 0.39 ; user 0.39 ; system 0.36 ; cuser 3.13 ; csystem 1.44