Hi!
I am running RAiSD analysis for the same vcf but with two different maf filtering:
600M Pop10_before_geo_cluster_005.vcf
1.3G Pop10_before_geo_cluster_001.vcf
This is the flags
-f Overwrites existing run files under the same run ID.
-M Indicates the missing-data handling strategy (0: discards SNP (default))
-y Provides the ploidy (integer value), in my case haploid
-w Provides the window size (integer value). The default value is 50 (empirically determined).
-c Provides the slack for the SFS edges to be used for the calculation of mu_SFS. The default value is 1 (singletons and S-1 snp class, where S is the sample size).
-s Generates a separate report file per set.
-I Provides the path to the input file, which can be either in ms or in vcf format.
#!/bin/sh
for i in *vcf*
do
/data/guido/RAiSD/raisd-master/bin/release/RAiSD -n ${i%.recode.vcf}_run -f -y 1 -M 0 -w 50 -c 1 -s -I $i
for n in $(seq 1 1 14)
do
echo $n
grep -v "//" RAiSD_Report.${i%.recode.vcf}_run.$n | awk -v dt=${i%.recode.vcf} -v nu=${n} '{print $0"\t"nu"\t"dt}' >> RAiSD_Report.ALL_runs_filtered.txt
done
done
These are the results. When I plot μ statistic value in the two graphs they differ by 8 order of magnitude (look y axis). I believe it is due to low frequency alleles but I can wrap my head around to explain why.
Can you please comment on these results and the applicability of RAiSD with the two maf filtering?
Thanks! Have a nice day
G.
Hi!
I am running RAiSD analysis for the same vcf but with two different maf filtering:
600M Pop10_before_geo_cluster_005.vcf
1.3G Pop10_before_geo_cluster_001.vcf
This is the flags
-f Overwrites existing run files under the same run ID.
-M Indicates the missing-data handling strategy (0: discards SNP (default))
-y Provides the ploidy (integer value), in my case haploid
-w Provides the window size (integer value). The default value is 50 (empirically determined).
-c Provides the slack for the SFS edges to be used for the calculation of mu_SFS. The default value is 1 (singletons and S-1 snp class, where S is the sample size).
-s Generates a separate report file per set.
-I Provides the path to the input file, which can be either in ms or in vcf format.
These are the results. When I plot μ statistic value in the two graphs they differ by 8 order of magnitude (look y axis). I believe it is due to low frequency alleles but I can wrap my head around to explain why.
Can you please comment on these results and the applicability of RAiSD with the two maf filtering?
Thanks! Have a nice day
G.