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printInfoFields does not display value of Type=Flag VCF INFO fields #2299

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heuermh opened this issue Feb 16, 2021 · 1 comment
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printInfoFields does not display value of Type=Flag VCF INFO fields #2299

heuermh opened this issue Feb 16, 2021 · 1 comment
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@heuermh
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heuermh commented Feb 16, 2021

DB Type=Flag VCF INFO field should be displayed as true/false

scala> printInfoFields(variants, Seq("DB", "dbsnp"))
Info Header Lines
INFO=<ID=DB,Number=0,Type=Flag,Description="Membership in dbSNP">
INFO=<ID=dbsnp,Number=1,Type=String,Description="dbSNP identifier">

Variant Info Fields
+----------------+--------+--------+-----+-----+----+--------------+
| Reference Name | Start  |  End   | Ref | Alt | DB |    dbsnp     |
+----------------+--------+--------+-----+-----+----+--------------+
|              1 | 865594 | 865595 | A   | G   |    |  rs903331232 |
|              1 | 874490 | 874491 | C   | T   |    | rs1441881282 |
|              1 | 877522 | 877523 | C   | G   |    |  rs200195897 |
|              1 | 878374 | 878375 | C   | T   |    |              |
|              1 | 879285 | 879286 | A   | C   |    |  rs770278990 |
|              1 | 879374 | 879375 | C   | T   |    |  rs761448939 |
|              1 | 881801 | 881802 | C   | T   |    |  rs777256112 |
|              1 | 890251 | 890252 | A   | G   |    |  rs185038034 |
|              1 | 896896 | 896897 | C   | T   |    |  rs777857163 |
|              1 | 897738 | 897739 | T   | C   |    |              |
+----------------+--------+--------+-----+-----+----+--------------+
@heuermh heuermh added this to the 0.34.0 milestone Feb 23, 2021
@heuermh
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heuermh commented Feb 23, 2021

Closing as not an issue, "DB" is not present in INFO attributes, it is mapped to the VariantAnnotation attribute dbSnp.

@heuermh heuermh closed this as completed Feb 23, 2021
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