Converts input bam and vcf files to a fragment matrix

• Pysam v.0.13

python3 FragMatrixCreator /path/to/bam /path/to/vcf genomic_region /output/folder

Fragment matrix /output/folder/genomic_region.frags

--output_prefix PREFIX      add prefix to output file: /output/folder/prefix_genomic_region.frags
--genotypes                 output additional /output/folder/genomic_region.genotypes file
--se                        set this flag if the reads are single-end

A fragment matrix always starts with with > sign and a genomic region name after it:
>scaffold2314|size104419
Next lines are fragments, their representation has 5 tab delimited columns:
NS500442:8:H194MBGXX:3:13604:2918:8976 352 00-00 F)-F@ 55

1. Read name
2. Start position (index of the corresponding polymorphic site in input vcf, 1-based)
3. Fragment sequence, 0 is REF, 1 is first ALT, 2 is second, etc., whereas - means no information available
4. Base call qualities in Phred+33 format

• In case of complex polymorphic sites with multiple bases the quality is mean(bases);
• The length of the quality string is equal to the fragment string, therefore if the fragment string contains missing alleles (-), the quality string will also have - on same positions. The dashes on other positions in quality string denote base quality 12 (ord('-') - 33).

5. Mapping quality

The fragments are separated by new lines.
Note: A fragment with only one allele may appear in a fragment matrix only if it has a mate with at least one different allele in the same genomic region
Some examples are shown in fragment_examples.txt.

(Output only if --genotypes flag is set)
Start with genomic region name:
>scaffold2314|size104419
Following with genotypes information from vcf file for every polymorphic sites:
1 0/0/1/1/1/1:96:38:1272:57:1673

1. Polymorphic site index (starting with 1 in every new genomic region)
2. GT column from vcf file

The genotypes are separated by new lines.