Update samtools parameters to improve indel calling

[katrinakalantar]

A recent issue was raised that we were missing some INDEL calls in the output .vcf files https://github.com/chanzuckerberg/idseq-workflows/issues/97

This PR does the following:

• addresses the issue by modifying the CallVariants step to use the -L and -d parameters to improve sensitivity for INDELS in the output .vcf files.
• passes the quality threshold that was used for CallConsensus to also be used in CallVariants consistent with recent changes upstream in the CZB sc2 pipeline.

This was tested offline using a sample with a known INDEL. The pipeline previously did not output the corresponding lines in the .vcf file, but the change has resulted in successful identification of the known INDEL.

[morsecodist]

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