# Read counts equals to 0 in indel mutations called by VarScan

**URL:** <https://help.galaxyproject.org/t/read-counts-equals-to-0-in-indel-mutations-called-by-varscan/1921>\
**Category:** usegalaxy.eu support\
**Tags:** variant-analysis\
**Created:** [August 13, 2019, 8:11am UTC](https://help.galaxyproject.org/t/read-counts-equals-to-0-in-indel-mutations-called-by-varscan/1921 "2019-08-13T08:11:46Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![SusanD](https://avatars.discourse-cdn.com/v4/letter/s/d26b3c/32.png) [@SusanD](https://help.galaxyproject.org/u/SusanD)\
**Post date:** [August 13, 2019, 8:11am UTC](https://help.galaxyproject.org/t/read-counts-equals-to-0-in-indel-mutations-called-by-varscan/1921/1 "2019-08-13T08:11:46Z")

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Dear Galaxy,

As I used the VarScan to call variants, I realized that many of the output lines that were called as indel mutation had the read counts information (i.e. AD, DP, FREQ, ADF, ADR, etc.) equals to 0.

I reviewed those positions with bam file on igv, and I did see that there were reads mapped to those positions. Is there an explanation for this?

Thanks a lot,

Susan