Does picard MergeBamAlignment function require paired reads as ALIGNED_BAM? This is not mentioned in the picard documents
However, we use trimmomatic to do reads QC, which generates three outputs: paired reads, unique reads after QC for 1st reads and 2nd reads. Then we use bwa to map three files individually to generate three sam files. Next, we merged bwa results into one bam file using picard MergeSamFiles. At last, we try to create a clean-up mapping file using picard MergeBamAlignment with a unmapped_bam file created from input fastq reads files using picard FastqToSam. The sort order of files are correct.
Does this mean picard and/or GATK does not work with a mixture of paired-reads and single-reads maps?
Hi. I'm unable to use the IndelRealigner java jar. My previous steps were;
1) Convert Bowtie2 paired-end Illumina Reads .sam to .bam
2) Use bedtools to extract pairs that fall within the Hg19 exome.
3) Convert the new .bam to .sam
4) Sort the new .sam via SortSam.jar
5) Mark duplicates via MarkDuplicates.jar
6) Use AddOrReplaceReadGroups.jar
7 ) Use ReorderSam.jar
8) Use RealignerTargetCreator
Untill this far everything went well. Now I'm trying the following command; java -jar GenomeAnalysisTK.jar -T IndelRealigner -R [.fasta] -l [ReorderedSam.bam] -targetIntervals [aligner.intervals] -o output.bam (Also when applying -known and an .vcf file Im producing the same error):
I hope you can help me, because I can't find anything related on google.