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BGI-shenzhen / PopLDdecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
MIT License
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Noise in LD Decay Plot #22

Open meeranhussain opened 1 week ago

meeranhussain commented 1 week ago

Hi,

I've been using PopLDdecay to analyze LD decay across multiple populations (7), but I'm noticing a wavy pattern in the decay curve that seems unusual. I would like to achieve a smoother LD decay plot and am reaching out for any suggestions or advice on improving this output. image

Commands used: /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat HAM_stat.gz -SubPop pop_files/HAM_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat NOR_stat.gz -SubPop pop_files/NOR_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat LIN_stat.gz -SubPop pop_files/LIN_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat INV_stat.gz -SubPop pop_files/INV_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat IRE_stat.gz -SubPop pop_files/IRE_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat FEAasw_stat.gz -SubPop pop_files/FEAasw_pop.txt -MAF 0.05 -MaxDist 1000 /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/PopLDdecay -InVCF M_aethio_popgen_all_bialSNP_MAF_geno.vcf -OutStat MOSSasw_stat.gz -SubPop pop_files/MOSSasw_pop.txt -MAF 0.05 -MaxDist 1000

Plotting

perl /nesi/nobackup/uow03744/Population_genomics_Maethio/01_Popgen_all/03_Analysis/05_stats/07_LD_decay/PopLDdecay-3.43/bin/Plot_MultiPop.pl -inList Multipop.txt -output M_aethio_popgen_all_LD_decay -bin1 1000 -break 10000 -bin2 1000 -keepR

Would you be able to suggest any modifications or specific parameters that could help reduce this waviness in the curve?

Thank you for your assistance!

hewm2008 commented 1 week ago

try: 1000-->5000 PopLDdecay-3.43/bin/Plot_MultiPop.pl -inList Multipop.txt -output M_aethio_popgen_all_LD_decay -bin1 5000 -break 10000 -bin2 5000 -keepR -maxX 200

Increasing -bin1 and -bin2 can indeed reduce it. But you have grown to 1000 and there are still fluctuations. This must be related to the quality of your ref. The quality of your ref assembly is not good. There may be some N-region lengths in the middle of the scaffold that are seriously inconsistent with the actual situation. -maxX 200