Entering edit mode
23 months ago
beausoleilmo
▴
600
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?