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