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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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Corrupt BAM files being produced in 0.9.9.37 #60

Closed tseemann closed 4 years ago

tseemann commented 4 years ago 
% MapCaller -r ref.fna -f R1.fq.gz -f2 R2.fq.gz -bam output.bam

% samtools index output.bam 

[E::hts_idx_push] Unsorted positions on sequence #1: 2430950 followed by 2422939
samtools index: failed to create index for "output.bam"

Maybe I forgot you produced unsorted BAMs ?

hsinnan75 commented 4 years ago

Yes, they are unsorted since MapCaller output BAM format as reads are aligned. They are ordered by the read order.