Does GATK4 v4.1.1.0 support MarkDuplicates?

I've run GATK3.5 with `MarkDuplicates`, but can't get it to run with GATK4 v4.1.1.0. I double-checked the best practices for data pre-processing for variant discovery and noted that the command `MarkDuplicates` still appears there. When I checked the tool documentation index I could pull up `MarkDuplicates` for GATK4 v4.0.8.0, but not v4.1.1.0. So I'm wondering if `MarkDuplicates` is supported by GATK4 v4.1.1.0?

Command:
```
strings=(
S1233686
)
for i in "${strings[@]}"; do
echo "${i}"

# Mark duplicates
/ast/emb/software/gatk-4.1.1.0/gatk MarkDuplicates \
I=/ast/emb/prjt3/aligned_data/${i}Aligned.sortedByCoord.out.bam \
O=/ast/emb/prjt3/aligned_data/${i}.dedupped.bam \
CREATE_INDEX=true \
VALIDATION_STRINGENCY=SILENT \
METRICS_FILE=/ast/emb/prjt3/aligned_data/dedup.metrics.${i}.txt


done
```

Output:
```
USAGE: MarkDuplicates [arguments]

Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads
are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library
construction using PCR. See also MarkDuplicates for
detailed explanations of the output metrics.
Version:4.1.1.0


Required Arguments:

--INPUT,-I:String One or more input SAM or BAM files to analyze. Must be coordinate sorted. This argument
must be specified at least once. Required.

****************REMOVED STANDARD HELP INFO TO SHORTEN OUTPUT****************************

Invalid argument 'I=/ast/emb/prjt3/aligned_data/S1233686Aligned.sortedByCoord.out.bam'.
Tool returned:
1
```

The output suggests that `MarkDuplicates` is supported. I hope I didn't make a silly syntax error. I did double-check that my input file exists.
Tagged:

Best Answer

  • embemb
    Accepted Answer
    After leaving this and coming back to it, I realize that I did make a silly mistake when updating my script. I called `ast/emb/software/gatk-4.1.1.0/gatk` where I needed to call `ast/emb/software/picard-2.18.16-0/picard.jar`.

    Maybe this will help someone else. . . .

Answers

  • embemb Member
    Accepted Answer
    After leaving this and coming back to it, I realize that I did make a silly mistake when updating my script. I called `ast/emb/software/gatk-4.1.1.0/gatk` where I needed to call `ast/emb/software/picard-2.18.16-0/picard.jar`.

    Maybe this will help someone else. . . .
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @emb

    You are absolutely right that this will help the community and thank you so much for contributing! We appreciate it. :smile:

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