Which fields/TAGS does strelka use?

[ksahlin]

Hello,

I am developing a short read aligner strobealign and would like to call variants using strelka. However, compared to, e.g., BWA, strelka reports no variations for strobealing's SAM file (as described here ), despite it having many properly paired primary alignments. I'm sure I have just missed outputting important TAGs or that the quality values are missing.

Could you help me with the following three questions, or alternatively, point me to the place in the paper or manual where I could find this information?

1. Does strelka need the quality values field?
2. Could you point me to any relevant optional tags TAGS that strelka uses so that I can add them?
3. Which of the SAM FLAGs does strelka use?

I have below posted BWA record and a strobealign record of the same read.

Thank you for your time, Kristoffer

BWA record (cut into multiple lines for visibility)

A00604:20:HHCFFDMXX:1:2155:14705:6104   99      Chr01   2       60      4M1D136M        =       134     272
ATATTTTAATGTCTTATAACTTCCGAATTCAAACTCAAATATTTGAATGTCTTATAACTTCCTTATTCAAACTTAAGGTAAAGAAATTCTTACCATTATATAAAAGTTTACCATCTTTATCTTGTTTAGGATTAGTGATA    
FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 
AS:i:131        XS:i:19 MQ:i:60 MC:Z:140M       ms:i:5070       MD:Z:4^A89T46   NM:i:2  RG:Z:line

Strobealign record of the same read (cut into multiple lines for visibility)

A00604:20:HHCFFDMXX:1:2155:14705:6104   99      Chr01   3       60      140M    =       134     271
ATATTTTAATGTCTTATAACTTCCGAATTCAAACTCAAATATTTGAATGTCTTATAACTTCCTTATTCAAACTTAAGGTAAAGAAATTCTTACCATTATATAAAAGTTTACCATCTTTATCTTGTTTAGGATTAGTGATA
*       
MQ:i:60 MC:Z:33=1X46=1X59=      ms:i:35700      MD:Z:0T0A0T0A89T46 NM:i:5