When I run BaseRecalibrator, my input reference file is genome.fa, my mapped file is K1_bam.marked.realigned.fixed.bam and variants/dbSNP file is New.vcf. the commands are showed as follows:
java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -I K1_bam.marked.realigned.fixed.bam -R genome.fa -knownSites New.vcf -o recal_dataK1.grp
Here is the result:
#####ERROR MESSAGE: Input files /raid1/rzeng/reference/New.vcf and reference have incompatible contigs: No overlapping contigs found. #####ERROR /raid1/rzeng/reference/New.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X] #####ERROR reference contigs = [chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]
Here my reference contig order is obviously different from variants files. How can I adjust the order of reference file and make it the same as New.vcf file? Also, my .bam file is a mapped file by aligning sample sequencing reads with reference file, so .bam should has the same chromosome order as reference file, do I need to to adjust the chromosome order of .bam file too, So confused here!