# \#bwa

**URL:** https://help.galaxyproject.org/tag/bwa/161.md

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## [BWAmeth: No option available to select the reference genome. Solution: Indexes available at usegalaxy.eu](https://help.galaxyproject.org/t/bwameth-no-option-available-to-select-the-reference-genome-solution-indexes-available-at-usegalaxy-eu/7272)

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**Author:** [@ssusmani](https://help.galaxyproject.org/u/ssusmani)\
**Replies:** 4\
**Last updated:** [August 26, 2022, 1:20pm UTC](https://help.galaxyproject.org/t/bwameth-no-option-available-to-select-the-reference-genome-solution-indexes-available-at-usegalaxy-eu/7272 "2022-08-26T13:20:49Z")

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Hi, I am going through the tutorials of DNA methylation analysis and once I have selected the bwa-meth for alignment. There is no option available to select the refence genome. I am also attaching a screeshot.

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## [problem with using BWA on usegalaxy.org](https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319)

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**Author:** [@kct913](https://help.galaxyproject.org/u/kct913)\
**Replies:** 1\
**Last updated:** [April 5, 2020, 6:32am UTC](https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319 "2020-04-05T06:32:26Z")

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I was trying to align 2 fastqsanger files that was trimmed using to FASTQ Quality trimmer (window size 4, average score \>=20) to the hg19 reference genome using BWA. But I got the following error message from galaxy job …

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## [BCFtools Mpileup Qual=0](https://help.galaxyproject.org/t/bcftools-mpileup-qual-0/1893)

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**Author:** [@SANJAY](https://help.galaxyproject.org/u/SANJAY)\
**Replies:** 6\
**Last updated:** [August 20, 2019, 2:08pm UTC](https://help.galaxyproject.org/t/bcftools-mpileup-qual-0/1893 "2019-08-20T14:08:40Z")

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Hi Galaxy Community members, I mapped fastq.gz files with ref genome using BWA MEM and then used BCFtools mpileup to generate vcf file for downstream variant detection using varscan. When I look at this vcf file, the qu…

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## [Create a Galaxy workflow to identify polymorphic sites in three individuals data - BWA error](https://help.galaxyproject.org/t/create-a-galaxy-workflow-to-identify-polymorphic-sites-in-three-individuals-data-bwa-error/599)

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**Author:** [@Abdul](https://help.galaxyproject.org/u/Abdul)\
**Replies:** 1\
**Last updated:** [February 12, 2019, 4:08pm UTC](https://help.galaxyproject.org/t/create-a-galaxy-workflow-to-identify-polymorphic-sites-in-three-individuals-data-bwa-error/599 "2019-02-12T16:08:49Z")

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workflow need to map the three sets of paired reads to the Human reference genome (hg19). I need to use a variant caller to identify sites that appear to have strong support for the presence of a polymorphism, and call t…

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## [Having issue with exome sequencing - Deprecated tool (BWA for Illumina) in older workflow](https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592)

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**Author:** [@Mo123](https://help.galaxyproject.org/u/Mo123)\
**Replies:** 3\
**Last updated:** [February 11, 2019, 1:29pm UTC](https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592 "2019-02-11T13:29:28Z")

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I uploaded my forward and reverse , I selected the hg19 and used bwa for short read to map . I get this error Could not display BAM file, error was: file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Con…