manhattan plot

[xqzangnolan]

HI,
I try to draw a manhattan plot, my plot just shows 300 SNP

my input file is the output file of pyseer( T304_SNPs_02_98.txt),

how can I find the input file with all of the SNP and with P value (not only the phenotype associated ones)?

My command:
pyseer --phenotypes T304_list.txt --vcf core.vcf.gz --load-m T304_mash_mds.pkl --lineage --print-samples --min-af 0.02 --max-af 0.98 > T304_SNPs_02_98.txt
15949 loaded variants
15625 pre-filtered variants
324 tested variants
324 printed variants
cat <(echo "#CHR SNP BP minLOG10(P) log10(p) r^2") <(paste <(sed '1d' T304_SNPs_02_98.txt | cut -d "_" -f 2) <(sed '1d' T304_SNPs_02_98.txt | cut -f 4) | awk '{p = -log($2)/log(10); print "26",".",$1,p,p,"0"}' ) | tr ' ' '\t' > T304_SNPs_02_98.plot

Waiting for your emails,
All the best,

[mgalardini]

Judging from your command it seems that most variatns get filtered because their allele frequency falls below/above the thresholds you have defined. What happens when you change the --min-af and --max-af arguments?