added optional -x flag for ivar trim. allows trimming of reads that occur at a specified offset position relative to the primer sequence positions #88
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…ccur at a specified offset position relative to the primer sequence positions
… for populate_from_file()
… for populate_from_file()
gkarthik
reviewed
Feb 5, 2021
| @@ -85,7 +85,7 @@ void print_bed_format(){ | |||
| std::cout << "It requires the following columns delimited by a tab: chrom, chromStart, chromEnd, name, score, strand" << std::endl; | |||
| } | |||
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| std::vector<primer> populate_from_file(std::string path){ | |||
| std::vector<primer> populate_from_file(std::string path, int32_t offset = 0){ | |||
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Given that offset will not be needed in most of the function calls, can you please overload this function instead of adding offset to every call?
stenglein-lab
added a commit
to stenglein-lab/viral_variant_caller
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Jul 26, 2022
1. Changed clipping penalty parameter in bwa mem from 5 to 1. This favors more soft-trimming at the ends of reads. Since variants at the ends of reads are less reliable, this reduces false-positive variant calling. 2. Expanded ivar trim trimming using the -x offset parameter. This trims extra bases around primer binding sites. This also makes variant calling more stringent. See these issues for more information on these settings: nf-core/viralrecon#170 andersen-lab/ivar#88
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In some amplicon-based sequencing protocols (e.g. SWIFT), polymerases can add additional bases, which can in turn lead mismatches. This PR includes a fix that allows users to specify an offset using the -x flag when running ivar trim. This is used to correctly trim reads that contain such polymerase-induced read artifacts.