Fan et al. 2022 #97
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Fan et al. 2022 #97
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standage
commented
Nov 10, 2022
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| rule get_hg37_coords: | ||
| input: | ||
| bed38="marker38.bed", | ||
| chain="hg38ToHg19.over.chain.gz", | ||
| output: | ||
| bed37="marker37.bed", | ||
| bedunmapped="marker-unmapped.bed", | ||
| shell: | ||
| """ | ||
| liftOver {input} {output} | ||
| [ ! -s {output.bedunmapped} ] | ||
| """ |
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Many of the SNPs/InDels don't have RSIDs, so positions for GRCh37 and GRCh38 must be provided explicitly. The authors provide only GRCh38 positions, so I whipped out UCSC's 38 --> 37 liftOver chain file for that conversion. Yay.
standage
commented
Nov 10, 2022
| data.sort_values('Marker').to_csv(output[0], sep='\t', index=False) | ||
| data.sort_values(['Marker', 'VariantIndex']).to_csv(output[0], sep='\t', index=False) |
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Made a slight change here...
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| mh06PK-24844 2 G GA | ||
| mh06FHL-001 2 C CATT | ||
| mh06FHL-001 7 A AC | ||
| mh06FHL-002 0 AT A,GT | ||
| mh06FHL-002 14 TG T | ||
| mh06FHL-002 25 C CA | ||
| mh06FHL-002 26 A AG | ||
| mh06PK-24844 1 C CT | ||
| mh06PK-24844 2 G GA |
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...to enforce a consistent order here.
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This looks like a Monday morning job... :) |
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No rush! |
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On second thought, please hold off on this. There's another massive PR I'd like to resolve first... |
added 2 commits
November 14, 2022 12:17
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Ok this is ready for review @rnmitchell! |
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Looks good! |
rnmitchell
approved these changes
Nov 14, 2022
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This branch adds a new marker collection from Fan et al. 2022. All 22 of these markers include SNPs with no RSIDs, so population frequency estimates based on 1000 genomes haplotypes cannot be determined.
Closes #93. Closes #95.