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bioinformatics-centre / BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers
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A question about convertAllele. #36

Closed zhiyongli1995 closed 3 years ago

zhiyongli1995 commented 3 years ago

Hi, I am using 'bayesTyperTools convertAllele' to convert my vcf file, in my alt column there are many type allele, then I trying add '--alt-file' in my code. I don't understand this description "alternative allele file (fasta format). Sequence name in fasta (>"name") should match <"name">. " I am not sure about my alt-file format. Looking forward to your reply! Best regards!

My code: bayesTyperTools convertAllele -v my.vcf -g Zm-B73-chr2.fa.masked --alt-file alt-seq.fa -o convert1.vcf

My error log:

[11/01/2021 22:29:21] Parsed 1 chromosome(s)
bayesTyperTools: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.5_static/BayesTyper-1.5/src/bayesTyperTools/ConvertAllele.cpp:79: void ConvertAllele::convertAllele(const string&, const string&, const string&, const string&, const string&, bool, bool): Assertion `alt_seqs.emplace("<" + cur_fasta_rec->id() + ">", make_pair(cur_fasta_rec, cur_fasta_rec_rv)).second' failed.
bayesConvert.sh: line 14: 14071 Aborted                 (core dumped)

My alt-seq.fa file head:

>INS
CCTTGTTTAGGGACTGGCAGGACACCCTAGACAACTCTAATCGACATAGAGTCTGTAACA
CCTGGGTTTTAAGGAACAAAGTCGGGTGCATCTCATACAT
>INS
ACTGTGTTCAGCGGTTCCCTCTAAATTTCTCCCCCTATATCTCACTCACGTGCCACGTCA
GCGTTCTCTTTCGCTCTATATCTCCACGCTCTACAGCGGTTCCCCCTATATCAAACCTCT
ATACCACACCACACCAATATTTTATACTTTCATCATCAACTAACTCAACTATCATCCAAT
ATTTGTTTTATTTTTATTTGCTCTATAAACAGTGCGCGGCCGTAACTTAGTACACAATTA
ATTAGCAAACTTCGTAAGCCTTGCCAAGCCAAAATCAGAAATCTTAGGCTTATAGTCATC
ATCAAGCAATATGCACTTGGAACTAATCTTAGGCTCATAGAATGCGAGGGTTGCAACTGT