RWhetten

Hi Pasi, Certainly - the attached file is the first five lines of the output from Pileup2Likelihoods. Regards, Ross

Hi Pasi, Thanks for the quick reply. My apologies for the misstatement of how I used Pileup2Likelihoods - I did use samtools mpileup with a list of BAM files to create the posterior probability file, then supplied that file to ParentCall2 with a pedigree file (attached). The commands were: samtools mpileup -q 10 -Q 10 -s -l regions.bed -b bam.list | java -cp ~/software/LepMap3/bin/ Pileup2Likelihoods > post.out java -cp ~/software/LepMap3/bin ParentCall2 data=pedigree.txt posteriorFile = post.out...

Hi Pasi, I used Pileup2Likelihoods to create a table of posterior probabilities from a VCF, with sample IDs S1 to S24 in the first line of the output file, but when I try to combine this with a pedigree file using ParentCall2, all 24 samples are reported as "not contained in the data" and all genotypes are set to missing. The pedigree file has the correct 6-line format, and 'cat -T ' shows only tab characters as delimiters in either the posterior probability table or the pedigree file. The top line...

I just realized the error is in providing the gzipped data file as input - using data=<(zcat data.post.gz) avoids the problem. Thanks!

Hi Pasi, The ParentCall2 command to convert VCF to genotype posteriors is java -cp ~/tools/lepmap3/bin ParentCall2 data=pedigree.txt vcfFile=input.vcf removeNonInformative=1 | bgzip -@8 > data.post.gz and the SeparateChromosomes2 command is java -cp ~/tools/lepmap3/bin SeparateChromosomes2 data=data.post.gz lodLimit=5 sizeLimit=10 lod3Mode=2 distortionLod=1 > sep.chrom.lod5.txt Thanks, Ross

Hi Pasi, I have a set of 30 haploid progeny from a single parent, and I called genotypes with BCFtools using a diploid model to identify regions of paralogous sequence with >3 heterozygous calls, so those could be filtered out. The pedigree file contains dummy male and female parents, and the VCF can be converted to posterior genotype probabilities without problems. SeparateChromosomes2 throws an error, and I can't find information in the forum about how to address this problem. The error is: java.lang.StringIndexOutOfBoundsException:...

Hi Pasi, Thanks for the quick reply. I'll try setting up a GNU parallel job to convert the BAM files to genotype likelihoods by scaffold and see how that works. Regarding coding - I don't have data for the diploid mother, so the pedigree (based on the example in the wiki) simply contains "male" and "female" in columns 3 & 4 of line 2, all samples listed as descended from "male" in line 3 and "female" in line 4, 0 for sample gender in line 5 and 0 for all in line 6. I'll try running OrderMarker2 with...

Hi Pasi, I have a set of 184 BAM files with data from haploid individuals segregating from a single diploid mother, and have produced a VCF file of biallelic SNPs by filtering the output of a variant-calling pipeline. I have a few questions about different aspects of the LepMap3 analysis. 1. I started an analysis with the pileupParser2.awk and pileup2posterior.awk scripts to compare that output with results from the VCF file, but that job has been running for over three weeks - is there any way to...