The current GATK version is 3.7-0
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2. Try the latest version of tools.
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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

BaseRecalibrator

Hi:
i met errors in my recalibration process.
every time errors occur, the messages put "don't post the errors",and then i can find solution in FAQ or furom.
however, this time, it tells me to post the errors. i tried to find sulotion, but failed.
i am new to GATK, and know little about java.

here is the command:

nohup java -Xmx50g -Djava.io.tmpdir=/tmp\
-jar $GATKdir/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-R ~/data/ReferAll/sortedIndex/ucsc.hg19.sorted.fasta \
-I ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam \
-knownSites ~/data/ReferAll/bundle/dbsnp_137.hg19.sorted.vcf \
-knownSites ~/data/ReferAll/bundle/1000G_phase1.indels.hg19.sorted.vcf \
-knownSites ~/data/ReferAll/bundle/Mills_and_1000G_gold_standard.indels.hg19.sorted.vcf \
-o ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam.recal.grp \

~/projects/TWINS/WGC007813/no.BaseRecalibrator.out &

and this is the errors message!


Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Okay, the good news is that you don't need to know any java to run GATK :)

    So, it looks like some of your reads have a CIGAR string that is causing errors. You may be able to bypass this issue by adding -rf BadCigar to your command. Let me know if that doesn't work.

    Also, in future, can you please just copy and paste the text of the errors, rather than give a screenshot? It is better for several reasons which I won't go into.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Okay, the good news is that you don't need to know any java to run GATK :)

    So, it looks like some of your reads have a CIGAR string that is causing errors. You may be able to bypass this issue by adding -rf BadCigar to your command. Let me know if that doesn't work.

    Also, in future, can you please just copy and paste the text of the errors, rather than give a screenshot? It is better for several reasons which I won't go into.

  • Hi: Auwera!
    thank you so much!! i solved my problem as you told me add "-rf BadCigar" option, i am sorry about the screenshot; until you replied to me did i realize that it's difficult to read my problem clearly because of the text composing, and pics which were not showing. i am sorry!!and thank you!

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