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Merge pull request #211 from replikation/customBED
Custom bed
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# source | ||
* V1200 bp scheme from: | ||
https://zenodo.org/record/3897530#.X4QxOpqxUay | ||
* V1200 bp scheme from: https://zenodo.org/record/3897530#.X4QxOpqxUay | ||
* Primers V to V4* -> https://github.com/artic-network/artic-ncov2019 | ||
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They are just copied here for workflow stability and ease of use. | ||
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# IMPORTANT | ||
+ PRIMER DIRS NEED TO START WITH A "V" | ||
+ BED FILES structure | ||
``` | ||
MN908947.3 22 46 varskip-0317-1_01_LEFT nCoV-2019_1 + | ||
``` | ||
* first column MN908947.3 (the fasta header of the reference) | ||
* 4th colum sort it (sort -k4) | ||
* also remove _alt might be problematic | ||
* 5th needs to be nCoV-2019_1 or nCoV-2019_2 | ||
`awk '{if (NR%4==0 || NR%4==3){print $1"\t"$2"\t"$3"\t"$4"\tnCoV-2019_2\t"$6} else {print $1"\t"$2"\t"$3"\t"$4"\tnCoV-2019_1\t"$6}}'` | ||
* 6th is + or - but can be skipped |
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Data from: https://github.com/nebiolabs/VarSkip |
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data/external_primer_schemes/nCoV-2019/V_custom/nCoV-2019.reference.fasta
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data/external_primer_schemes/nCoV-2019/V_custom/nCoV-2019.reference.fasta.fai
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MN908947.3 29903 12 60 61 |
296 changes: 148 additions & 148 deletions
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data/external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.scheme.bed
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