other reference in BaseRecalibrator known-sites option
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8
b) Exact command used: BaseRecalibrator
c) Entire error log:
A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17,
features contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.
I used Korean reference on mapped NA12878
Then I want to run GATK4 BaseRecalibrator, but I can write BaseRecalibrator --known-sites option.
I know for the BaseRecalibrator to work, that option is required.
how can I make Korean reference known sites??
I look up a few things, lift-over is a solution. right??
but I have no chain file of Korean reference to GRCh38.
how can I solve this problem?
Thank you
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add
when I did LiftoverVcf, it has the error
log
...
INFO 2020-10-08 16:07:28 LiftOver Interval chr1:108359162-108359163 failed to match chain 1069 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
INFO 2020-10-08 16:07:28 LiftOver Interval chr1:108371701-108371702 failed to match chain 1075 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
[Thu Oct 08 16:07:28 KST 2020] picard.vcf.LiftoverVcf done. Elapsed time: 6.52 minutes.
Runtime.totalMemory()=12119441408
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.checkBounds(String.java:383)
at java.lang.String.<init>(String.java:324)
at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:301)
at picard.vcf.LiftoverVcf.tryToAddVariant(LiftoverVcf.java:558)
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:453)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:301)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)thank you
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BI_joy you will need a valid chain file from GRCh38 to the reference you are using to get this to work.
Here is a good explanation from UCSC: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
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Genevieve Brandt (she/her) Thank you for letting me know.
I will refer to it and study.thank you
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