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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

Fishy output from ReduceReads

I've been following the best practices guide and I've gotten some odd looking output from ReduceReads. Here's a sample:

C100 16 chrM 4934 60 1M * 0 0 T 7 BD:Z:E RG:Z:JC01_L1 BI:Z:L RR:B:c,1 RS:A:1

The odd part is the CIGAR string. Is "1M" a reasonable CIGAR string? Furthermore, prior to ReduceReads, Picard tools' ValidateSamFile finished with no errors, and the validation for the ReduceReads output is like so:

WARNING: Record 1, Read name 1, NM tag (nucleotide differences) is missing

That occurs for records 1 - 100 and then ValidateSamFile does not report any more.

Here is the command line I used for ReduceReads:

java -Xmx2g -Djava.io.tmpdir=pwd/tmp -jar $GATK -T ReduceReads -R $genomes/hg19.fa -I $alignments/$lane.dedup.realn.recal.bam -o $alignments/$lane.dedup.realn.recal.reduced.bam

Note that pwd is surrounded by back ticks, I just don't know how to disable them from interrupting the code format.

Any advice?

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Answers

  • blakeoftblakeoft ConnecticutMember

    Thank you for your answer, Geraldine. I misunderstood what ReduceReads actually does. I went back and watched the presentation and it all makes sense now.

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