updated rule filter (in merge_samples) #64
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…h the most samples
| import os | ||
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| for file in input: | ||
| shell("wc -l {file} >> files_len.txt") |
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This sorts by the number of lines - which is SNPs, not samples. Is this ok?
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I guess this is about the number of individuals, correct @gmafrafortuna ? We could probably extract the number of individuals using vcf/bcftools. I also found this awk one-liner: awk '{if ($1 == "#CHROM"){print NF-9; exit}}' input_vcf_file.vcf This looks at the #CHROM line in the vcf file which is the line of the column header (which includes individual names).
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so it starts from the file with the most samples