Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file.
C1_lenght=155648 AAAGATAGAGA.. C2_lenght=125018 ATGGATC... etc.. I have done alignments without problem, but for GATK : I do rmdup --> CreateSequenceDictionary.jar (picard) --> samtools sort --> Read Group (picard) --> samtools index and then : Pre alignment with :
java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -nt 8 -T RealignerTargetCreator -R REF.fa -o RTC.intervals -I INPUT_muq30_RMDUP_RG.bam
Here there is no problem, but when I want to make the realignement :
java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -T IndelRealigner -R REF.fa -I INPUT_muq30_RMDUP_RG.bam -targetIntervals RTC.intervals -o INPUT_muq30_RMDUP_RG_REAL.bam
And I got this error message : ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '13'
I didn't find any explanation in google for this error. Could you please help me ?!
Hi, I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas GATK (inspite of its several steps to prepare the BAM for variant caller) takes forever. I understand my reference is large and since its an exome capture the targeted region is only 60 Mbp of 1.3Gbp. RealignerTargetCreator is the step it takes forever to locate for sites where indel realignment is required. Do someone have any suggestions to speed it up? Or try any other variant caller? I have tried downsampling my BAM with samtools view -s and that too takes as the log says 8 more days to finish :(
Here is my sample command:
java -Xmx20g -XX:MaxPermSize=40G -jar /software/production/gatk/2.3.9/x86_64/GenomeAnalysisTK.jar -T RealignerTargetCreator -I in.bam -R ref.fa -o out.bam
Hi, using unified genotyper with multiple samples (different lines of Medicago truncatula showing polymorphism), I would like to get a file giving me, for each sample, the alleles at each SNP position (SNP positions identified for all samples). Is it possible? I didn't find any option for this, and it would be dificult to make SNP calling for each sample and then create a new file with all of them, because SNPs positions and number are different according to the samples. Thanks in advance,