# Open gvcf files

**URL:** <https://discuss.hail.is/t/open-gvcf-files/2991>\
**Category:** Hail Query & hailctl\
**Created:** [December 14, 2022, 3:18pm UTC](https://discuss.hail.is/t/open-gvcf-files/2991 "2022-12-14T15:18:18Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ofer](https://avatars.discourse-cdn.com/v4/letter/o/a4c791/32.png) [@Ofer](https://discuss.hail.is/u/Ofer)\
**Post date:** [December 14, 2022, 3:18pm UTC](https://discuss.hail.is/t/open-gvcf-files/2991/1 "2022-12-14T15:18:18Z")

</div>

Hi,

I’m trying to open a gvcf file as a matrix table, but I’m not sure that I’m doing it in the right way.  
I’m defining the partitions by the regions list:

```python
CHR_RANGES = {'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259,
              'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422,
              'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189,
              'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167,
              'chr21': 46709983 , 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415}

regions = [hl.parse_locus_interval("[chr1:1-chr1:248956422]")]
for chrom in CHR_RANGES.keys():
    if chrom != 'chr1':
        interval = hl.parse_locus_interval("[" + chrom + ":1-" + chrom + ":" + str(CHR_RANGES[chrom]) + "]")
        regions.append(interval)

```

Then:

```python
PKGen160 = hl.import_gvcfs(['gvcf_path'], partitions=regions)

```

And these are the first 10 rows of the matrix table that I got:

 ![image](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/1X/b3228ecee9fd78d7946f25f9a924a9f1d189d991.png)

Is it ok?

Thanks,  
Ofer

---

<div class="post-metadata">

**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [December 16, 2022, 3:24pm UTC](https://discuss.hail.is/t/open-gvcf-files/2991/2 "2022-12-16T15:24:38Z")

</div>

Hey @Ofer !

Apologies! This part of our API is very new and not well documented.

To directly answer your question: `import_gvcfs` just efficiently imports many GVCFs as many distinct Hail Tables. You want the docs for [`VariantDataset`](https://hail.is/docs/0.2/vds/index.html) and the [`VariantDatasetCombiner`](https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.VariantDatasetCombiner):

```python
gvcfs = [
    'gs://bucket/sample_10123.g.vcf.bgz',
    'gs://bucket/sample_10124.g.vcf.bgz',
    'gs://bucket/sample_10125.g.vcf.bgz',
    'gs://bucket/sample_10126.g.vcf.bgz',
]

combiner = hl.vds.new_combiner(
    output_path='gs://bucket/dataset.vds',
    temp_path='gs://1-day-temp-bucket/',
    gvcf_paths=gvcfs,
    use_genome_default_intervals=True,
)

combiner.run()

vds = hl.read_vds('gs://bucket/dataset.vds')

```

* * *

A few extra comments:

1. [`hl.locus_interval`](https://hail.is/docs/0.2/functions/genetics.html#hail.expr.functions.locus_interval) is easier to use in this case than `hl.parse_locus_interval`:

```plaintext
hl.locus_interval(chrom, 1, CHR_RANGES[chrom])

```

1. Hail can give you chromosomal metadata directly:

```python
hl.contig_length(chrom)

```

1. You can also access the `ReferenceGenome` object directly with [`get_reference`](https://hail.is/docs/0.2/api.html#hail.get_reference).

```python
gr = hl.get_reference("GRCh37")

```