Callableloci And I Argument

Question

[Peyman]

Hi, I am trying to run the following: T CallableLoci -R ucsc.hg19.fasta -I myreorder.bam -L SureSelectAllExon50mbwithannotationhg19.bed -o CLmmq30mbq20cov45 --minMappingQuality 30 --minBaseQuality 20 --minDepth 45 --summary /home/nejat/bamfile/CLmmq30mbq20_cov45.summary

but it breaks with this message:

ERROR MESSAGE: Invalid command line: Argument -I has a bad value: CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: [org.broadinstitute.sting.gatk.datasources.sample.Sample@0]

could you plz help me?

Answer 1

[Sean Davis]

Just a guess, but your BAM file might have more than one sample in it. You can take a look using:

samtools view -H

Answer 2

[Peyman]

Thanks. its fine. but after the following: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R /ucsc.hg19.fasta -I /outmerge_reorder_rg.bam -L /SureSelect_All_Exon_50mb_with_annotation_hg19.bed -o /realignment.intervals -B:dbsnp,VCF /dbsnp_132.hg19.vcf -B:indels,VCF /1000G_indels_for_realignment.hg19.vcf

it breaks with: ERROR MESSAGE: Invalid command line: The parameter rodBind is deprecated. Bindings for reference-ordered data, in the form :[?],[?] [?]

Plz help me in this matter.

Amin