Cannot get AddOrReplaceReadGroups to run

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Robert Butler

• February 12, 2020 21:20

GATK version 4.0.12

Trying to merge several bams and run `HaplotypeCaller`, but that gives a `java.lang.IllegalArgumentException: samples cannot be empty` error. Ran `ValidateSamFile` and got the `ERROR:MISSING_READ_GROUP`. So trying to fix that with `AddOrReplaceReadGroups`, but I cannot find any possible combination of syntax to get it to run. Example:

```gatk --java-options "-Xmx360G" AddOrReplaceReadGroups \
-I $merge_bam \
-O $merge_bam2 \
-LB bar \
-PL illumina \
-PU foo \
-SM merged \
-CREATE_INDEX True
```

Returns `Invalid argument 'bar'.`
Full commands:

```

# merge bams
gatk --java-options "-Xmx360G" MergeSamFiles \
--USE_THREADING true \
--arguments_file $bams_to_merge\
-O $merge_bam

# samtools merge -f -@ $threads -b $bams_to_merge $merge_bam
gatk --java-options "-Xmx360G" AddOrReplaceReadGroups \
-I $merge_bam \
-O $merge_bam2 \
-LB bar \
-PL illumina \
-PU foo \
-SM merged \
-CREATE_INDEX True

#############call variants##############
# merge calls
samtools index -@ $threads $merge_bam
gatk --java-options "-Xmx360G" HaplotypeCaller \
-R $genome_ref \
-D $dbSNP \
--genotyping-mode DISCOVERY \
-stand-call-conf 30 \
-I $merge_bam \
-O $merge_vcf

```

0

• 

  Robert Butler

  • February 13, 2020 01:57

  I updated to gatk4.1.4.1 and the command ran without issue.

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• 

  Bhanu Gandham

  • February 15, 2020 18:23

  Thank you for the update Robert Butler

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