If anyone can explain this I would appreciate it.
I ran blasr on some pacbio ccs data in fasta format. I then attempted to use freebayes to call variants on the resulting bam file.
Code:
freebayes -F 0.5 --pooled-continuous -f ref.fa -C 3 pacbio_ccs_reads.fa-vs-ref.fa.sort.bam >pacbio_ccs_reads.fa-vs-ref.fa.sort.bam.vcf
Code:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NO_CHIP_ID ref 3659 . TAT TT 15.2798 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1M1D1M;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=4;MQM=254;MQMR=0;NS=1;NUMALT=1;ODDS=3.48821;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=-34;PRO=1;QA=0;QR=0;RO=0;RPL=1;RPP=5.18177;RPPR=0;RPR=3;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=del GT:[B]DP[/B]:DPR:[B]RO[/B]:QR:[B]AO[/B]:QA:GL 1/1:[B]7[/B]:7,4:[B]0[/B]:0:[B]4[/B]:0:-3.145,-4.65015,0
Any ideas?
Thanks
Addendum:
Now if I do the same thing with the run's subreads (fastq format) I get a freebayes result that is much more in keeping with what I see in the bam alignment data (though not exact, at least it reflects the low variant occurence relative to the reference occurence). WTF.