GATK Indelrealignment Problem : The input is truncated?

Question

[sevvalakturk96]

After realigning with bam files with GATK Indelrealigner , we are getting error: "EOF marker is absent.The input is probably truncated."

We did that before with other bam files and there wasn't any problem ,but now we are in trouble. We though that it can be due to insufficient memory. To solve it we split the bam files by chromosomes and tried realignment again. It didn't work. We got the same error. For all of these, GATK 3.2 was used. Here our code :

java -Xmx65000m -jar /usr/local/sw/GenomeAnalysisTK.jar -T IndelRealigner -R x.fa -I input.bam  -known x.vcf.gz -targetIntervals  x.intervals -o output.bam

Any suggestions ?

Answer 1

[kanika.151]

I would do sam to bam conversion again or repeat the last step again which created your input.bam.