autocorrelation?

[cistarsa]

Hello and thank you for this nifty program! I'm using it to determine relatedness among three sympatric populations (within ~5mi radius) across two years and find an extremely high level of relatedness among all individuals. I'm using the r0, r1 and king-robust values for visualization but I'm concerned at the seemingly perfect correlation between these values among the individuals. Below is the angsd code used to generate the likelihoods. The reference genome is large at >2Gb, so I mapped the low coverage reads (1-3x) to the first half of the genome.

#map fastqs to reference:
bwa-mem2 mem -t32 noCont.fasta "$in1" "$in2" | samtools view -bS - | samtools sort - > sample."$z".bam

# did not mark duplicates, could this drive the difference?

#angsd.
angsd -b 176.temp -gl 2 -nInd 176 -minInd 158 -doCounts 1 -setMaxDepth 1580 -rf chrom5.rf.list -setMinDepth 320 -setMinDepthInd 1 -setMaxDepthInd 10 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -nThreads 8 -out chrom5_90pc

#ngsrelate.
ngsRelate -g chrom5_90pc.glf.gz -n 176 -z 176.20201.list -f 179_chrom5.freq -O 179_chrom5_out

[cistarsa]

moved on