samtools having to use -A input option

Question

[williamsbrian5064]

Hi,

I am using samtools to make a bcf file and then a vcf file. I am using the following code

samtools mpileup --redo-BAQ --min-BQ 30 --per-sample-mF -C 50 --output-tags DP,DV,DPR,INFO/DPR,DP4,SP -A -u -f Felis_catus.Felis_catus_9.0.dna_sm.toplevel.fa --BCF C04893_L001.sorted.dedup.bam > C04893.bcf

I have used samtools on a number of samples and never had to use the -A input option. For some reason, one of my samples wouldn't start making a the bcf file without using the -A input option. I was curious why what happened all of the sudden? I was wondering if anyone had a similar issue? Is there a way to see if there is something weird about the bam file? Would samtools flagstat tell me anything?

[finswimmer]

Hello,

could you please show the output of samtools flagstat for a "normal" sample andbthe "weird" one?

fin swimmer

[swbarnes2]

The simple explanation is that there is something really different about that fastq file. Did you look up what -A meant before you asked this question?