new plugin: vcf2table

[lindenb]

Hi all,

This is a PR for a new plugin vcf2table which is the C version of my tool https://jvarkit.readthedocs.io/en/latest/VcfToTable/ .

This tool reads a VCF and output the variants as a set of ascii table.

eg:

bcftools +vcf2table ./test/merge.4.b.vcf

(...)
<<< 1:3000002:C (n. 5)

# Variant
┌────────┬─────────┐
│ KEY    │ VALUE   │
├────────┼─────────┤
│ CHROM  │ 1       │
│ POS    │ 3000002 │
│ ID     │ .       │
│ REF    │ C       │
│ ALT    │ A       │
│ QUAL   │ 59.2    │
│ FILTER │ PASS    │
└────────┴─────────┘

# INFO
┌─────┬─────┬───────┐
│ KEY │ IDX │ VALUE │
├─────┼─────┼───────┤
│ AN  │     │ 4     │
│ AC  │     │ 2     │
└─────┴─────┴───────┘

# GENOTYPE TYPES
┌──────┬───────┬─────┐
│ Type │ Count │ %   │
├──────┼───────┼─────┤
│ HET  │ 2     │ 100 │
└──────┴───────┴─────┘

# GENOTYPES
┌────────┬───────┬─────┬─────┐
│ SAMPLE │ GTYPE │ GT  │ GQ  │
├────────┼───────┼─────┼─────┤
│ C      │ HET   │ 0/1 │ 245 │
│ D      │ HET   │ 0/1 │ 245 │
└────────┴───────┴─────┴─────┘

>>> 1:3000002:C (n. 5)





bcftools +vcf2table test/split-vep.2.vcf 


<<< 1:14464:A (n. 1)

# Variant
+--------+---------+
| KEY    | VALUE   |
+--------+---------+
| CHROM  | 1       |
| POS    | 14464   |
| ID     | .       |
| REF    | A       |
| ALT    | T       |
| QUAL   | 2235.88 |
| FILTER | PASS    |
+--------+---------+

# INFO
+-----+-----+-------+
| KEY | IDX | VALUE |
+-----+-----+-------+
| AF  |     | 1     |
+-----+-----+-------+

# VEP/CSQ
+--------+------------------------------------+----------+---------+-----------------+-------------------+-----------------+------------------------+-------+-----------------------------+---------------+--------------------+------------+----------+--------+---------------+---------------+---------+-----------+--------+--------+--------+--------+--------+--------+--------+-------------+
| Allele | Consequence                        | IMPACT   | SYMBOL  | Gene            | Feature_type      | Feature         | BIOTYPE                | EXON  | HGVSc                       | cDNA_position | Existing_variation | ALLELE_NUM | DISTANCE | STRAND | VARIANT_CLASS | SYMBOL_SOURCE | HGNC_ID | CANONICAL | AF     | AFR_AF | AMR_AF | EAS_AF | EUR_AF | SAS_AF | MAX_AF | MAX_AF_POPS |
+--------+------------------------------------+----------+---------+-----------------+-------------------+-----------------+------------------------+-------+-----------------------------+---------------+--------------------+------------+----------+--------+---------------+---------------+---------+-----------+--------+--------+--------+--------+--------+--------+--------+-------------+
| T      | non_coding_transcript_exon_variant | MODIFIER | WASH7P  | ENSG00000227232 | Transcript        | ENST00000423562 | unprocessed_pseudogene | 10/10 | ENST00000423562.1:n.1568T>A | 1568          | rs546169444        | 1          |          | -1     | SNV           | HGNC          | 38034   |           | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | non_coding_transcript_exon_variant | MODIFIER | WASH7P  | ENSG00000227232 | Transcript        | ENST00000438504 | unprocessed_pseudogene | 12/12 | ENST00000438504.2:n.1682T>A | 1682          | rs546169444        | 1          |          | -1     | SNV           | HGNC          | 38034   | YES       | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | downstream_gene_variant            | MODIFIER | DDX11L1 | ENSG00000223972 | Transcript        | ENST00000456328 | processed_transcript   |       |                             |               | rs546169444        | 1          | 55       | 1      | SNV           | HGNC          | 37102   | YES       | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | non_coding_transcript_exon_variant | MODIFIER | WASH7P  | ENSG00000227232 | Transcript        | ENST00000488147 | unprocessed_pseudogene | 11/11 | ENST00000488147.1:n.1291T>A | 1291          | rs546169444        | 1          |          | -1     | SNV           | HGNC          | 38034   |           | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | non_coding_transcript_exon_variant | MODIFIER | WASH7P  | ENSG00000227232 | Transcript        | ENST00000538476 | unprocessed_pseudogene | 13/13 | ENST00000538476.1:n.1530T>A | 1530          | rs546169444        | 1          |          | -1     | SNV           | HGNC          | 38034   |           | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | non_coding_transcript_exon_variant | MODIFIER | WASH7P  | ENSG00000227232 | Transcript        | ENST00000541675 | unprocessed_pseudogene | 9/9   | ENST00000541675.1:n.1315T>A | 1315          | rs546169444        | 1          |          | -1     | SNV           | HGNC          | 38034   |           | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
| T      | regulatory_region_variant          | MODIFIER |         |                 | RegulatoryFeature | ENSR00000000002 | open_chromatin_region  |       |                             |               | rs546169444        | 1          |          |        | SNV           |               |         |           | 0.0958 | 0.0144 | 0.1138 | 0.005  | 0.1859 | 0.1943 | 0.1943 | SAS         |
+--------+------------------------------------+----------+---------+-----------------+-------------------+-----------------+------------------------+-------+-----------------------------+---------------+--------------------+------------+----------+--------+---------------+---------------+---------+-----------+--------+--------+--------+--------+--------+--------+--------+-------------+

# BCSQ
+-------------+--------+------------------------+
| Consequence | gene   | biotype                |
+-------------+--------+------------------------+
| non_coding  | WASH7P | unprocessed_pseudogene |
+-------------+--------+------------------------+

>>> 1:14464:A (n. 1)
(...)

Thank you for considering this PR.

[pd3]

Hi, we can add this. Can you add tests please?

[lindenb]

@pd3 Cool, thanks !

I found a memory leak and added the two examples above in test/test.pl . There are still some problems with win32 but as far as I understand, the problem is unrelated to my plugin.

Back to you. Thanks !

[pd3]

Thank you