I am interested in calling SNPs with mileup using de novo contigs generated from a Trinity run and reads aligned with Rsem.
I ran the following command but I got a segmentation fault
samtools mpileup -ugf mga_femalelimited_trinity.fas turkey_female_limited.transcript.sorted.bam
I generated the index for the fasta file separately with faidx and there was no error.
Any help would be much appreciated, thanks