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List Parental Mosaic

Description:

This function identifies putative parental-mosaic variant transmissions in a manner that (by default) keeps only high-confidence variants for further consideration. For each parent-child pair, it considers all variants that were transmitted from carrier parent to a carrier child.

Command examples:

atav.sh --list-parental-mosaic --sample PATH_TO_SAMPLE_FILE --min-child-binomial 0.001 --max-parent-binomial 0.000005 --out PATH_TO_OUTPUT_DIR

Command options:

--list-parental-mosaic: trigger list parental mosaic function.

--child-qd: specify a minimum child QD value.

--child-het-percent-alt-read: this filter will exclude the child het variants by the alt read freq.

--min-child-binomial: specify the minimum Binomial Exact one-tail p-value permitted for the childs alt:ref ratio discrepancy from expected 0.5

--max-parent-binomial: specify the maximum Binomial Exact one-tail p-value permitted for the parental alt:ref ratio discrepancy from expected 0.5

Note this function can accept a single parent.

The test itself relies on a one-tailed binomial exact test on the observed portion of reads that support the variant to determine the probability of obtaining such an outcome ratio given an expected proportion of 0.5.
Example R equivalent code, sample has 15 alternative alleles and 102 reference alleles: binom.test(15,117,p=0.5,alternative="less")$p.value = 2.2x10-17

For this function, the current recommended parameters are:

--ctrl-maf 0.0005 \
--evs-maf 0.0005 --evs-pop ea,all,aa \
--exac-maf 0.0005 --exac-pop global,afr,amr,eas,sas,fin,nfe \
--var-status pass+intermediate \
--exclude-evs-qc-failed \
--exclude-artifacts \
--qual 30 \
--mq 40 \
--rprs -4 \
--mqrs -8 \
--child-qd 2 \
--child-het-percent-alt-read 0.30-0.80 \
--min-child-binomial 0.001 \
--max-parent-binomial 0.000005 \

Output:

parental.mosaic.csv

  • Family Id
  • Sample Name (child)
  • Genotype (child)
  • Binomial (child)
  • Sample Name (parent)
  • Genotype (parent)
  • Binomial (parent)

Please check Output Columns for common columns.