freebayes, SNPs
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Hello all
I am facing a problem in FreeBayes, I am calling for variants in a haployid population. After I submit the job, the stdeerr file keeps increasing in size and it has error stating ‘Opened BAM reader without index file, jumping is disabled.
HISEQ:115:C49JYACXX:4:1206:9623:100139 at scaffold1|size923514:1 is out of order!
HISEQ:56:D1UAHACXX:2:1113:3701:14592 at scaffold1|size923514:2 is out of order!
HISEQ:115:C49JYACXX:4:1210:15069:58013 at scaffold1|size923514:1 is out of order!
so on…, I am not sure how long it takes to get the final vcf file. But for it keeps running for more than 20 days and job gets aborted due to internal issues. The size of vcf file is too high 40gigs.
Can you please help with the issue, this is my command I am using freebayes -0 --use-best-n-alleles 4 --ploidy 1 -C 2 --no-indels --no-mnps --no-complex –f ..bam.
As suggested by Erik Garrison i sorted and indexed the bam files, I still face the same problem. i am not sure whether to feed the index file or not and how to feed.
the script that i haven been using
freebayes -0 --use-best-n-alleles 4 --ploidy 1 -C 2 --no-indels --no-mnps --no-complex -f ../../assm_1kb.fasta -b 1.bam 2.bam ......bam > output.vcf
any help highly appreciated thanks in advance.
Prakash