<p>I have a vcf file created with GATK with spanning deletion <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-" rel="nofollow noreferrer">https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-</a> and I now need to compare this VCF with its gold standard using hap.py (<a href="https://github.com/Illumina/hap.py/blob/master/doc/happy.md#getting-started" rel="nofollow noreferrer">https://github.com/Illumina/hap.py/blob/master/doc/happy.md#getting-started</a>) but the spanning allele gives me the following error:</p>
<p><code>[W] too many AD fields at chr10:133017183 max_ad = 2 retrieved: 3</code> and I've read that is due to * in the ALT column.</p>
<p>So, is there a way to convert the spanning alleles into simple vcf files?</p>
<p>Thanks a lot,
Denise</p>

CC BY-SA 4.0
2021-02-23T15:16:27.563Z
Could you describe what problems you're having? You could try using `rtg-tools vcfeval` since it's designed to account for differences in indel representation between the truthset and callset.
user438383
CC BY-SA 4.0
2021-02-23T16:03:52.853Z
Thanks a lot, I know I can use it but I would like to follow the best practises given by the Global Alliance for Genomics and Health Benchmarking Team (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699627/)
Denise Lavezzari
CC BY-SA 4.0
2021-02-27T18:42:33.660Z
Please [edit] your question and include some of the offending lines. Also make sure to include the relevant headers since the headers are where this sort of thing is defined. We can't really help without seeing the file.
terdon
<vcf><indel>
Spanning deletion conversion
# Spanning deletion conversion

(Asked by: username_0 on 2021-02-23)

I have a vcf file created with GATK with spanning deletion <https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-> and I now need to compare this VCF with its gold standard using hap.py (<https://github.com/Illumina/hap.py/blob/master/doc/happy.md#getting-started>) but the spanning allele gives me the following error:

`[W] too many AD fields at chr10:133017183 max_ad = 2 retrieved: 3` and I've read that is due to \* in the ALT column.

So, is there a way to convert the spanning alleles into simple vcf files?

Thanks a lot,
Denise

**Tags:** vcf, indel
> **Comments:**
> **username_1**: Could you describe what problems you're having? You could try using `rtg-tools vcfeval` since it's designed to account for differences in indel representation between the truthset and callset.  
> **username_0**: Thanks a lot, I know I can use it but I would like to follow the best practises given by the Global Alliance for Genomics and Health Benchmarking Team (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699627/)  
> **username_2**: Please [edit] your question and include some of the offending lines. Also make sure to include the relevant headers since the headers are where this sort of thing is defined. We can't really help without seeing the file.  

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## 0 answers

