Daily build

MAKE_OBS_TAB.py

@@ -86,10 +86,10 @@ def retrive_bases(bam_filename,legend_filename,fasta_filename,handle_multiple_ob
         pos = 0
         for pileupcolumn in samfile.pileup(**arg):
 
-            while pileupcolumn.pos > pos-1:  ### Chromosomal position starts from 1 in legend table, while it starts from 0 in the pileup iterator.
+            while pileupcolumn.reference_pos > pos-1:  ### Chromosomal position starts from 1 in legend table, while it starts from 0 in the pileup iterator.
                 chr_id,pos,ref,alt = next(leg_tab_iterator)
 
-            if pileupcolumn.pos == pos-1:
+            if pileupcolumn.reference_pos == pos-1:
 
                 rows = [obs_tuple(pos, pileupread.alignment.query_name, pileupread.alignment.query_sequence[pileupread.query_position])
                         for pileupread in pileupcolumn.pileups if pileupread.query_position!=None] # query_position is None if the base on the padded read is a deletion or a skip (e.g. spliced alignment).

pipeline.txt

@@ -110,9 +110,15 @@ The script `MAKE_REF_PANEL.py` creates reference panels for LD-PGTA, using phase
 
 We run the script with the following arguments and flags:
 
-`python3 MAKE_REF_PANEL.py EUR_panel.samples ALL.chr21.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz`,
+`python3 MAKE_REF_PANEL.py EUR_panel.samples ALL.chr21.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz --mask 20160622.chr1.mask.fasta.gz`,
 
-where the first argument is the IMPUTE2 SAMPLE file. The second required argument is a VCF filename that correspond to a single chromosome. 
+where the first argument is the IMPUTE2 SAMPLE file. The second required argument is a VCF filename that correspond to a single chromosome. The third argument an accessibility mask file in a gzipped FASTA format and is optional. Supplying an accessibility mask file will reduce false SNPs in regions of the genome that are less accessible to NGS methods. [GRCh38 genome accessibility masks for 1000 Genomes data](https://www.internationalgenome.org/announcements/genome-accessibility-masks/) are available from: [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/20160622_genome_mask_GRCh38/](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/20160622_genome_mask_GRCh38/). 
+
+In addition, the following flags are supported:
+
+`--output-directory <PATH>` _The directory in which the reference panel would be created._
+
+`--force-module cyvcf2/pysam` _By deafult cyvcf2 module would be used. This allows to use pysam instead._
 
 # Tabulation of allele observations at known SNPs #
 <a name="obs_tab"/>
@@ -304,7 +310,7 @@ The next step is to convert the reference panel VCF to BCF format:
 `--exclude-types indels,mnps,ref,bnd,other \`\
 `--min-alleles 2 \`\
 `--max-alleles 2 \`\
-`--min-ac 1 \`\
+`--min-ac 1:minor \`\
 `--phased \`\
 `--exclude 'AN!=2*N_SAMPLES' \`\
 `--output-file chr21_EUR_panel.bcf \`\