Hello,
I did the "lofreq call" as usual:
firstly, I have assessed the quality of alignement with code:
./lofreq indelqual --dindel -f reference.fa -o file_indelqual.bam file.bam
I got the "file_indelqual.bam" file
Secondly, I used this code to obtain the vcf :
./lofreq call -f + reference.fa --call-indels -o nom.vcf file_indelqual.bam
after this code, it displays:
FATAL(plp.c|mpileup:1420): Reference fasta file doesn't seem to contain the right sequence(s) for this BAM file. (mismatch for seq XXX listed in BAM header)
I recheck the samtools, there is no pbl for .sam to .bam
I can not understand where is the pbl.
Hello, I did the "lofreq call" as usual: firstly, I have assessed the quality of alignement with code: ./lofreq indelqual --dindel -f reference.fa -o file_indelqual.bam file.bam
I got the "file_indelqual.bam" file
Secondly, I used this code to obtain the vcf : ./lofreq call -f + reference.fa --call-indels -o nom.vcf file_indelqual.bam
after this code, it displays: FATAL(plp.c|mpileup:1420): Reference fasta file doesn't seem to contain the right sequence(s) for this BAM file. (mismatch for seq XXX listed in BAM header)
I recheck the samtools, there is no pbl for .sam to .bam I can not understand where is the pbl.
Do you have some ideas for solving this pbl?
thanks