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Good day.I
![cannot open controllerData_b dat](https://github.com/user-atta…
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I am new to Regenie and trying to test it on my dataset. here's my setting in step1:
regenie \
--step 1 \
--bed chr22_prune \
--keep lowtg_samples.txt \
--covarFile pheno.txt \
--pheno…
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@gregorgorjanc @RosCraddock
Originally, while estimating the alternative allele frequency of the whole population, the algorithm looped over the genotypes of all the individuals to calculate the most…
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Good evening,
`ngsPool` provides `poolSFS.R`, a script which estimates a one dimensional SFS from the `SAF.GZ` output file. Is it possible for other software to read pairs of "sample allele frequen…
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Hi
I have simulated some haploid data with Illumina error rates and ancient DNA data. It is ~25x coverage.
I wanted to see how the damage influences heterozygosity/genotype calls.
I noticed that …
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Hello,
I successfully ran est_p, and am now trying to estimate the hybrid index using default settings. The data for the putative hybrids is formatted the same way as the parentals, but I am gettin…
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[VariantContextUtils](https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java) currently calculates allele frequencies using AC/AN, but thes…
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Hi,
I am a new user of the `coloc` package and need clarification on how to correctly set up input parameters, particularly `MAF`, `N`, and `sdY`. I am working with GWAS and eQTL data, where the GW…
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So we can change allele freq in the founders (not setting to 0.5 and not estimating from the data)
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I am using CNVkit to call somatic CNAs from tumor-normal paired WES data. The BAM files were generated using GATK pipeline and the somatic VCF file was called using Mutect2 pipeline. However, I am get…