Elize Ng

Bootstrapping running into erorr 'Use of uninitialized value in division (/)'

2

Hi all, I have successfully ran my psmc for a few species, the regular run works out fine with no errors. and now I am running the bootstrapping segment of...

Old pipeline deprecated, using bcftools consensus instead?

3

The pipeline to generate the input for psmc has always been `samtools mpileup -C50 -uf ref.fa aln.bam | bcftools view -c - | vcfutils.pl vcf2fq -d 10 -D 100 |...

Output from bcftools consensus in .fq format

4

I am trying to run PSMC to obtain demographic history, and am looking to call consensus sequences from my study samples. PSMC requires a ".fq.gz" input which is typically the...

Simulate IBD for known relationships

1

Hi, I am working on a dataset that potentially has related individuals and would like to determine which relatedness analysis is best suited for my dataset. Is there any way...

Trouble running SCAT with huge dataset

9

I am having trouble executing SCAT with my SNP dataset consisting of more than ~18k loci for both assigning individuals and estimating allele frequencies. My file format is formatted as...

Defining multiple polygons in continuous assignment

1

Hi, I am working with a species that has a huge range that includes multiple islands, and am wondering if it is possible to define boundary polygons that specify each...