Ancestral fasta file missing

[krostifangers]

Hello
I tried to run the tutorial of selectiontool pipeline.
multipop_selection_pipeline -p CEU_ids.txt -p YRI_ids.txt -i CEU_YRI_lactase.vcf --config-file ~/Applications/selectionTools/defaults.cfg -a "--phased-vcf" -c 2

on test data (SelectionPipelineTestData/lactase ) stops returning the last message in multi_population.log as follow:

selection_pipeline STDERR: UnboundLocalError: local variable 'ancestral_fasta' referenced before assignment.

I noticed that this issue was previously reported. However I cannot find the reference fasta file in the Referencefile/ancestral_ref/ folder (just an ANCESTRAL.rst empty file). So where can I find this ancestor fasta file?
As the vcf used in the tutorial is already annotated for ancestral allele, is it necessary to have such a fasta file for ancestor?
Thank you in advance
All the best
Christophe

[murraycadzow]

Hi Christophe,

As the pipeline is setup the ancestral reference is needed. The link in the documentation in the getting started section will get you to down load this file ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.tar.bz2
although the most recent version for GRCh37 I know about is ftp://ftp.ensembl.org/pub/release-75/fasta/ancestral_alleles/homo_sapiens_ancestor_GRCh37_e71.tar.bz2

that needs to be extracted into the empty directory you mention and then in your config file you need to update the section about the ancestral reference to be specific to your files.

While the example vcf has the ancestral allele annotated, this is not always the case, especially when supplying your own data.

regards
Murray