I am trying to run pixy to calculate pi on a masked vcf file that will often have one haplotype masked (i.e. marked as missing) while the other haplotype has genotype data (i.e. 1 or 0). I dont get any errors when running pixy but the output will always have "NA" because it thinks all pairwise comps contain missing data. Output will look like:
pop chromosome window_pos_1 window_pos_2 avg_pi no_sites count_diffs count_comparisons count_missing
Ngoye NC_035107.1 379329 399328 NA 0 0 0 8265
Angola NC_035107.1 379329 399328 NA 0 0 0 6175
I am running:
for chr in {1..3}; do
pixy --stats pi fst dxy \
--vcf chr${chr}_Angola_Ngoye.2hap.vcf.gz \
--populations Ngoye.Angola.samplemap \
--n_cores 4 \
--bed_file chr${chr}_Angola_Ngoye.2hap_20k.bed \
--output_prefix chr${chr}_Angola_Ngoye.2hap --bypass_invariant_check yes; done
my vcf file looks like:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Debug010_aegypti_Cuanda_Angola_02 Debug010_aegypti_Cuanda_Angola_05 Debug010_aegypti_Cuanda_Angola_06 Debug010_aegypti_Cuanda_Angola_08 Debug010_aegypti_Cuanda_Angola_09 Debug010_aegypti_Cuanda_Angola_10 Debug010_aegypti_Cuanda_Angola_11 Debug010_aegypti_Cuanda_Angola_12 Debug010_aegypti_Cuanda_Angola_14 Debug010_aegypti_Cuanda_Angola_16 Debug010_aegypti_Cuanda_Angola_17 Debug010_aegypti_Cuanda_Angola_19 Debug010_aegypti_Cuanda_Angola_20 Debug024_aegypti_Ngoye_Senegal_F_10 Debug024_aegypti_Ngoye_Senegal_F_11 Debug024_aegypti_Ngoye_Senegal_F_12 Debug024_aegypti_Ngoye_Senegal_F_16 Debug024_aegypti_Ngoye_Senegal_F_1 Debug024_aegypti_Ngoye_Senegal_F_20 Debug024_aegypti_Ngoye_Senegal_F_3 Debug024_aegypti_Ngoye_Senegal_F_8 Debug024_aegypti_Ngoye_Senegal_M_13 Debug024_aegypti_Ngoye_Senegal_M_14 Debug024_aegypti_Ngoye_Senegal_M_15 Debug024_aegypti_Ngoye_Senegal_M_17 Debug024_aegypti_Ngoye_Senegal_M_18 Debug024_aegypti_Ngoye_Senegal_M_6 Debug024_aegypti_Ngoye_Senegal_M_9
Hello, thanks for making such a useful tool!
I am trying to run pixy to calculate pi on a masked vcf file that will often have one haplotype masked (i.e. marked as missing) while the other haplotype has genotype data (i.e. 1 or 0). I dont get any errors when running pixy but the output will always have "NA" because it thinks all pairwise comps contain missing data. Output will look like:
pop chromosome window_pos_1 window_pos_2 avg_pi no_sites count_diffs count_comparisons count_missing Ngoye NC_035107.1 379329 399328 NA 0 0 0 8265 Angola NC_035107.1 379329 399328 NA 0 0 0 6175
I am running: for chr in {1..3}; do pixy --stats pi fst dxy \ --vcf chr${chr}_Angola_Ngoye.2hap.vcf.gz \ --populations Ngoye.Angola.samplemap \ --n_cores 4 \ --bed_file chr${chr}_Angola_Ngoye.2hap_20k.bed \ --output_prefix chr${chr}_Angola_Ngoye.2hap --bypass_invariant_check yes; done
my vcf file looks like:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Debug010_aegypti_Cuanda_Angola_02 Debug010_aegypti_Cuanda_Angola_05 Debug010_aegypti_Cuanda_Angola_06 Debug010_aegypti_Cuanda_Angola_08 Debug010_aegypti_Cuanda_Angola_09 Debug010_aegypti_Cuanda_Angola_10 Debug010_aegypti_Cuanda_Angola_11 Debug010_aegypti_Cuanda_Angola_12 Debug010_aegypti_Cuanda_Angola_14 Debug010_aegypti_Cuanda_Angola_16 Debug010_aegypti_Cuanda_Angola_17 Debug010_aegypti_Cuanda_Angola_19 Debug010_aegypti_Cuanda_Angola_20 Debug024_aegypti_Ngoye_Senegal_F_10 Debug024_aegypti_Ngoye_Senegal_F_11 Debug024_aegypti_Ngoye_Senegal_F_12 Debug024_aegypti_Ngoye_Senegal_F_16 Debug024_aegypti_Ngoye_Senegal_F_1 Debug024_aegypti_Ngoye_Senegal_F_20 Debug024_aegypti_Ngoye_Senegal_F_3 Debug024_aegypti_Ngoye_Senegal_F_8 Debug024_aegypti_Ngoye_Senegal_M_13 Debug024_aegypti_Ngoye_Senegal_M_14 Debug024_aegypti_Ngoye_Senegal_M_15 Debug024_aegypti_Ngoye_Senegal_M_17 Debug024_aegypti_Ngoye_Senegal_M_18 Debug024_aegypti_Ngoye_Senegal_M_6 Debug024_aegypti_Ngoye_Senegal_M_9
NC_035107.1 379329 . C T . . AF=0.0706806;CM=0.209779;AN=23;AC=13 GT ./. ./. ./. 1/. ./. ./. 0/. ./. ./../. ./. 0/. ./. 0|1 1/. 0|1 1|1 1|0 .|1 ./. 1|1 ./. ./. 0|1 1|0 0|0 1|0 ./.
Bed file: NC_035107.1 379329 399328
Pops file: Debug024_aegypti_Ngoye_Senegal_F_10 Ngoye Debug024_aegypti_Ngoye_Senegal_F_11 Ngoye Debug024_aegypti_Ngoye_Senegal_F_12 Ngoye Debug024_aegypti_Ngoye_Senegal_F_16 Ngoye Debug024_aegypti_Ngoye_Senegal_F_1 Ngoye Debug024_aegypti_Ngoye_Senegal_F_20 Ngoye Debug024_aegypti_Ngoye_Senegal_F_3 Ngoye Debug024_aegypti_Ngoye_Senegal_F_8 Ngoye Debug024_aegypti_Ngoye_Senegal_M_13 Ngoye Debug024_aegypti_Ngoye_Senegal_M_14 Ngoye Debug024_aegypti_Ngoye_Senegal_M_15 Ngoye Debug024_aegypti_Ngoye_Senegal_M_17 Ngoye Debug024_aegypti_Ngoye_Senegal_M_18 Ngoye Debug024_aegypti_Ngoye_Senegal_M_6 Ngoye Debug024_aegypti_Ngoye_Senegal_M_9 Ngoye Debug010_aegypti_Cuanda_Angola_02 Angola Debug010_aegypti_Cuanda_Angola_05 Angola Debug010_aegypti_Cuanda_Angola_06 Angola Debug010_aegypti_Cuanda_Angola_08 Angola Debug010_aegypti_Cuanda_Angola_09 Angola Debug010_aegypti_Cuanda_Angola_10 Angola Debug010_aegypti_Cuanda_Angola_11 Angola Debug010_aegypti_Cuanda_Angola_12 Angola Debug010_aegypti_Cuanda_Angola_14 Angola Debug010_aegypti_Cuanda_Angola_16 Angola Debug010_aegypti_Cuanda_Angola_17 Angola Debug010_aegypti_Cuanda_Angola_19 Angola Debug010_aegypti_Cuanda_Angola_20 Angola