Hi,
I am a newbie working on mitochondria DNA sequencing. One error message I had during GATK quality score recalibration was " incompatible contigs Input files reads and reference have incompatible contigs: No overlapping contigs found.". My SAM files were aligned to the rCRS reference (gi|251831106|ref|NC_012920.1|), but the known SNP vcf files from NCBI FTP has contig MT. I tried to replace gi|251831106|ref|NC_012920.1| with MT in my SAM and reference files, but the same error message remained. Any ideas?
Codes:
index the reference FASTA
tmap index -f ~/refseq/RCRS.fa samtools faidx ~/refseq/RCRS.fa
Default TMAP alignment
tmap mapall -f ~/refseq/RCRS.fa -r ~/ion_torrent/fastq/IonXpress_002_XXX.fastq -v stage1 map1 map2 map3 > ~/ion_torrent/map123/0403/SAM/sample1_normal.sam
Convert SAM to BAM
samtools view -bS ~/ion_torrent/0403/map123/SAM/sample1_normal.sam > ~/ion_torrent/0403/map123/BAM/sample1_normal.bam
Sort and index BAM file
samtools sort ~/ion_torrent/0403/map123/BAM/sample1_normal.bam ~/ion_torrent/0403/map123/BAM/sample1_normal.sorted.bam samtools index ~/ion_torrent/0403/map123/BAM/sample1_normal.sorted.bam
java -Xmx8000m -Djava.io.tmpdir\=tmp -jar /bin/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -T BaseRecalibrator -R ~/refseq/RCRS.fa -I ~/ion_torrent/0403/map123/BAM/sample1_normal.sorted.bam -knownSites ~/refvcf/MT-1409-CEU.vcf -o ~/ion_torrent/0403/map123/GRP/sample1_normal.recal.grp -plots sample1_normal.recal.grp.pdf
