I have already mapped my data with STAMPY/ However, I'm trying to map with BWA in order to use GATK. I am running BWA 0.7.12 on a linux cluster.
I first built my reference index:
bwa index reference.fa
Then I tried to run the alignment:
bwa mem -M - reference.fa single_end_read_file.fq > test_aligned_reads.sam
And receive the following error:
[bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!
I'm not quite sure what to do as BWA created the indices it says don't work together. Any suggestions would be helpful. Thanks.