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khanabadosh@KhanaBadosh:/mnt/c/Users/Abhishek Kumar/Desktop/NGS_Data_Analysis/Test1$ java -Xmx2g -jar abra2-2.23.jar --in Sorted_out.bam --out
Sorted_out.abra.bam --ref S288C_reference_sequence_R64-…
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On a Ubuntu base image, if I try to use the precompiled `abra2-2.24.jar`, using command:
```
java -jar abra2-2.24.jar --in input.bam --out out.abra.bam --ref reference.fa --threads 2 --tmpdir /tmp…
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My bed file with its one-line header made abra2 crash with the following error:
Loading target regions from : target.bed
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at …
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Producing this error with our own bams using v0.79 built on Mountain Lion. However, using the demo bam and bed file included with abra runs perfectly.
Command:
java -Xmx16G -jar $JAR --in $inputBam …
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I'm attempting to run a HaplotypeCaller job that requires that the BAM and BAI file are in the same directory. However, for some reason Cromwell is putting the inputs into separate subdirectories. For…
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I am running Abra-0.96 using abra-0.96-SNAPSHOT-jar-with-dependencies.jar
It runs over 24 hours and gives me the following error:
Clock time in Align and clean contigs: 49461
Sat Dec 19 21:10:43 CST…
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GATK is throwing an error because it complains about ReadGroups. This [BioStar](https://www.biostars.org/p/115819) might have some solutions on how to overcome this.
``` java
root@2f68d7ec1b12:/home…
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ABRA version - 0.96
Platform - CentOS
command used to run ABRA
`java -Xmx4G -jar abra-0.96-SNAPSHOT-jar-with-dependencies.jar --in C26.bam --out C26.ABRA.bam --ref hs37d5.fa --targets Agilent_Nimblege…
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Le bouton annuler est totalement décalé car dans un bloc POST différent. Il faudrait le réaligner si possible.
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Excerpt from PiscesBioinformaticsApplicationNote_SupplementaryMethods.docx:
"The highest quality results can be obtained by using an indel-realigned, stitched bam."
"The full Pisces Suite workfl…