I have population sequencing (125bp SE) of an organism, and I have managed to find large indels spanning several kb with bbmap tools. See here how the data looks when the .sam file is visualized.
It looks like some might even be supported by 2 reads or more (same start same stop).
Is there anyway to call these? What software would you recommend? I tried freebayes, but I can't get any calls for some reason.
I tried the following commands with samtools:
samtools mpileup -d 250 -m 1 -E --BCF --output-tags DP,DV,DP4,SP -f RefAnnotated_SPades_HXE-3.fasta -o mapped_AdaptTrim_trial1.bcf mapped_AdaptTrim.sort.bam
bcftools index mapped_AdaptTrim_trial1.bcf
bcftools call --skip-variants snps --multiallelic-caller --variants-only -O v mapped_AdaptTrim_trial1.bcf -o mapped_AdaptTrim_trial1_vcf.vcf
However, the detected indels are not too long, maximum 50-100bp. The ones I am seeing in the image posted are a few kb in length.