How to convert a Beagle file 3.3 to VCF with beagle2vcf.jar?
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Entering edit mode
7 weeks ago
beausoleilmo ▴ 500

I imputed a beagle file using beagle like this:

java -jar beagle.jar \
            like=beaglein.gz \
            out=my 

Making a marker file and chromosome file

zcat my.gprobs.gz | awk 'NR>2  {print $1, $2, $3}' > my.markers_original.txt
zcat my.gprobs.gz | awk 'NR>2  {print $1}' > my.chrom.txt

Then I wanted to convert the beagle3.3 output t a vcf with beagle2vcf.jar

java -jar beagle2vcf.jar \
          chrom=my.chrom.txt \
          markers=my.markers_original.txt \
          bgl=my.gprobs.gz \
          missing=? 

But I always get

Picked up JAVA_TOOL_OPTIONS: -Xmx2g
java.io.FileNotFoundException: bgl= my.gprobs.gz (No such file or directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at blbutil.InputStreamIterator.fromGzipFile(InputStreamIterator.java:143)
        at beagleutil.Beagle2Vcf.readBglIdLine(Beagle2Vcf.java:215)
        at beagleutil.Beagle2Vcf.printVcfHeader(Beagle2Vcf.java:208)
        at beagleutil.Beagle2Vcf.main(Beagle2Vcf.java:58)
Error opening bgl= my.gprobs.gz

But the "my.gprobs.gz" file is really present. What is going on? How can this program work?

conversion vcf beagle • 112 views
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