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<macros>
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        <requirements>
            <requirement type="package" version="1.2">samtools</requirement>
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                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
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            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
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                @misc{Danecek_et_al,
                Author={Danecek, P., Schiffels, S., Durbin, R.},
                title={Multiallelic calling model in bcftools (-m)},
                url = {http://samtools.github.io/bcftools/call-m.pdf},}
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                @misc{Durbin_VCQC,
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                title={Segregation based metric for variant call QC},
                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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                @misc{Li_SamMath,
                Author={Li, H.},
                title={Mathematical Notes on SAMtools Algorithms},
                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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                @misc{SamTools_github,
                title={SAMTools GitHub page},
                url = {https://github.com/samtools/samtools},}
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    <xml name="version_command">
        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error" />
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    <token name="@no-chrom-options@">
-----

.. class:: warningmark

**No options available? How to re-detect metadata**

If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:

1. Click on the **pencil** icon adjacent to the dataset in the history
2. A new menu will appear in the center pane of the interface
3. Click **Datatype** tab
4. Set **New Type** to **BAM**
5. Click **Save**

The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.

    </token>

</macros>