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@fellen31
fellen31 committed May 15, 2024
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Expand Up @@ -59,7 +59,7 @@ You will need to create a samplesheet with information about the samples you wou

It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below.
`file` can either be a gzipped-fastq file or an aligned or unalinged BAM file (BAM files will be converted to FASTQ and aligned again).
`phenotype` is not used at the moment but still required, set it to `1`. If you don't have related samples, set `family_id`, `paternal_id` and `maternal_id` to something of your liking which is not a `sample` name.
`phenotype` is not used at the moment but still required, set it to `1`. If you don't have related samples, `family_id` could be set to sample name, and `paternal_id` and `maternal_id` to a value that is not another `sample` name.

If sex is unknown, a VCF of known polymorphic sites (e.g. [sites.hg38.vcg.gz](https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz)) needs to be supplied with `--somalier_sites`, from which sex will be inferred if possible.

Expand All @@ -69,18 +69,15 @@ HG002,/path/to/HG002.fastq.gz,FAM,HG003,HG004,1,1
HG005,/path/to/HG005.bam,FAM,HG003,HG004,2,1
```

| Fields | Description |
| ------------------------------------------ | ---------------------------------------------------------------------------------------------------------- |
| `sample` | Custom sample name, cannot contain spaces. |
| `file` | Absolute path to gzipped FASTQ or BAM file. File has to have the extension ".fastq.gz", .fq.gz" or ".bam". |
| `family_id` | "Family ID must be provided and cannot contain spaces. If no family ID is avail |
| able, use the same ID as the sample. |
| `paternal_id` | Paternal ID must be provided and cannot contain spaces. If no paternal ID is a |
| vailable, use any ID not in sample column. |
| `maternal_id` | Maternal ID must be provided and cannot contain spaces. If no maternal ID is a |
| vailable, use any ID not in sample column. |
| `sex` | Sex (0=unknown; 1=male; 2=female). |
| `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). |
| Fields | Description |
| ------------- | ------------------------------------------------------------------------------------------------------------------------- |
| `sample` | Custom sample name, cannot contain spaces. |
| `file` | Absolute path to gzipped FASTQ or BAM file. File has to have the extension ".fastq.gz", .fq.gz" or ".bam". |
| `family_id` | "Family ID must be provided and cannot contain spaces. If no family ID is available you can use the same ID as the sample |
| `paternal_id` | Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use any ID not in sample column. |
| `maternal_id` | Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use any ID not in sample column. |
| `sex` | Sex (0=unknown; 1=male; 2=female). |
| `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). |

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

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