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Include contig and position in SNP list #23

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CarolineOhrman opened this issue May 26, 2020 · 0 comments
Open

Include contig and position in SNP list #23

CarolineOhrman opened this issue May 26, 2020 · 0 comments
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enhancement New feature or request

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@CarolineOhrman
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CarolineOhrman commented May 26, 2020

Copying issue from CanSNPer adrlar/CanSNPer#28 (comment)

@standage commented

When I use the --snp_list option, I get a report like this.

#SNP Derived Ancestral ft-asmbl.fna

B.1     T       C       T
B.2     T       G       T
B.3     T       C       T
B.4     A       T       T
B.5     T       C       T
B.6     T       C       C
B.7     G       A       A
B.8     T       G       G
B.9     C       T       T

I've been looking at the snp_lister function trying to figure out if there's any convenient way to include the contig ID and position aligned to that SNP.

#SNP    Derived Ancestral       ft-asmbl.fna     QuerySeq        QueryPosition
B.1     T       C       T       contig1 XXX
B.2     T       G       T       contig1 XXX
B.3     T       C       T       contig2 XXX
B.4     A       T       T       contig3 XXX
B.5     T       C       T       contig4 XXX

Would this be possible?

@CarolineOhrman CarolineOhrman added the enhancement New feature or request label May 26, 2020
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