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Project description
Python pakcage for genomic variant analysis
variant-effect
command can infer the effect of a mutation
- The input file has 4 columns:
chromosome
,position
,reference allele
,alternative allele
. No header is required.
eg:
chr16 400560 G T
chr17 41690930 G T
chr6 61574496 A T
chr2 84906522 G T
chr2 216205243 G T
chr4 73455665 G T
chr2 101891316 G T
chr2 69820761 G T
chr6 30723661 A T
- The output can be stdout stdout, or a file.
#chrom pos ref alt mut_type gene_name transcript_id transcript_pos transcript_motif coding_pos codon_ref aa_pos aa_ref
chr16 400560 G T ThreePrimeUTR NME4 ENST00000219479 806 GCACCAAAGTGCCGGACAACC None None None None
chr17 41690930 G T Substitution EIF1 ENST00000591776 515 CTTGTATAATGTAACCATTTG 363 ATG 121 M
chr6 61574496 A T Intergenic None None None None None None None None chr2 84906522 G T ThreePrimeUTR TMSB10 ENST00000233143 312 AAGCTGCACTGTGAACCTGGG None None None None
chr2 216205243 G T ThreePrimeUTR XRCC5 ENST00000392133 2701 TGCCATCGCTGTGATGCTGGG None None None None
chr4 73455665 G T Substitution AFP ENST00000226359 1836 TTCATTCGGTGTGAACTTTTC 1820 TGT 607 C
chr2 101891316 G T ThreePrimeUTR MAP4K4 ENST00000350878 4267 GGAATTCCTTGTAACTGGAGC None None None None
chr2 69820761 G T Substitution ANXA4 ENST00000394295 934 AAATTGACATGTTGGATATCC 846 ATG 282 M
chr6 30723661 A T Substitution TUBB ENST00000327892 754 GATGAGACCTATTGCATTGAC 599 TAT 200 Y
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