Commit 14602a3a authored by eboulanger's avatar eboulanger
Browse files

clean up

parent b221f7e4
SNP filtering results for Diplodus sargus
ddocent pipeline + additions
filtering step filter for individuals retained SNPs retained run time (sec) output
step 0 ddocent output data 297 13362 sar_ddocent.vcf
step 1 call below 50%, mac < 3, min quality score = 30 297 13362 14.00 g5mac3.recode.vcf
step 2 min mean depth genotype call = 3 297 13362 14.00 g5mac3dp3.recode.vcf
step 3 remove individuals > 50% missing data 297 13362 16.00 g5mac3dplm.recode.vcf
step 4 remove sites > 5% missing data, maf 0.05, min meanDP = 5 297 10389 11.00 DP3g95maf05.recode.vcf
step 5 filter for allele balance 297 10202 DP3g95maf05.fil1.vcf
step 6 filter out sites with reads from both strands SKIP SKIP SKIP
step 7 ration of mapping qualities reference vs alternate alleles 297 9689 DP3g95maf05.fil3.vcf
step 8 paired status 297 9689 DP3g95maf05.fil4.vcf
step 9 remove sites quality score < 1/4 depth 297 9688 DP3g95maf05.fil5.vcf
step 10 depth x quality score cutoff 297 8325 11.00 DP3g95maf05.FIL.recode.vcf
step 11 He > 0.6 & Fis > 0.5 & Fis < -0.5 297 8206 27 min DP3g95maf05.FIL.HFis.recode.vcf
step 12 rename dip_all_filtered.vcf
\ No newline at end of file
SNP filtering results for Mullus surmuletus
ddocent pipeline + additions
filtering step filter for individuals retained SNPs retained run time (sec) output
step 0 ddocent output data 431 49027 mullus.vcf
step 1 call below 50%, mac < 3, min quality score = 30 431 49027 71.00 mullus.g5mac3.recode.vcf
step 2 min mean depth genotype call = 3 431 49027 74.00 mullus.g5mac3dp3.recode.vcf
step 3 remove individuals > 50% missing data 424 49027 70.00 mullus.g5mac3dplm.recode.vcf
step 4 remove sites > 5% missing data, maf 0.05, min mean DP = 5 424 18727 14.00 DP3g95maf05.recode.vcf
step 5 filter for allele balance 424 17965 DP3g95maf05.fil1.vcf
step 6 filter out sites with reads from both strands SKIP SKIP SKIP
step 7 ration of mapping qualities reference vs alternate alleles 17546 DP3g95maf05.fil3.vcf
step 8 paired status 17546 DP3g95maf05.fil4.vcf
step 9 remove sites quality score < 1/4 depth 17546 DP3g95maf05.fil5.vcf
step 10 depth x quality score cutoff 15466 DP3g95maf05.FIL.recode.vcf
step 11 He > 0.6 & Fis > 0.5 & Fis < -0.5 15232 DP3g95maf05.FIL.Hfis.recode.vcf
step 12 rename mul_all_filtered.vcf
\ No newline at end of file
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