Using Mixcr for hybridization capture data?

[lmcbride053]

I have tried multiple different presets for processing hybrid-capture sequences in MiXCR using the analyze command and have not been able to retrieve the expected results. What sort of command/preset/features would you recommend using to process hybrid-capture data? I have seen some studies that have done it successfully.

[mizraelson]

Hi, can you describe in more detail the structure of your library?

[lmcbride053]

We used the Twist NGS Library Preparation Kits for our library preparation. Does that answer your question?

[mizraelson]

Have you tried the command bellow:

mixcr analyze exome-seq \
    --species hsa \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result

What command did you try and what was unexpected about the results?

Can you share the studies you have mentioned?

Sincerely,
Mark