MuTect --- with more stringent parameter settings I got more mutations -- Is this possible

Haiying7Haiying7 Heidelberg, GermanyMember

I ran MuTecct twice, once with default parameter settings, and the second time with stringent parameter settings.

default:
/usr/bin/java -Xmx4g -Djava.io.tmpdir=tmp -jar ${MuTect}mutect-1.1.7.jar \
--input_file:normal ${BQSR_dir}${Blood}.recal.bam --input_file:tumor ${BQSR_dir}${Nevus}.recal.bam \
--out ${MuTect_dir}${Blood}${Nevus}_call_stats.out \
--coverage_file ${MuTect_dir}${Blood}
${Nevus}coverage.wig.txt \
--vcf ${MuTect_dir}${Blood}
${Nevus}.vcf \
--analysis_type MuTect --reference_sequence ${GATK_hg} --cosmic ${COSMIC} --dbsnp ${dbSNP} --intervals ${Intervals} \
--disable_auto_index_creation_and_locking_when_reading_rods

stringent:
/usr/bin/java -Xmx4g -Djava.io.tmpdir=tmp -jar ${MuTect}mutect-1.1.7.jar \
--input_file:normal ${BQSR_dir}${Blood}.recal.bam --input_file:tumor ${BQSR_dir}${Nevus}.recal.bam \
--out ${MuTect_dir}${Blood}${Nevus}_call_stats.out \
--coverage_file ${MuTect_dir}${Blood}
${Nevus}coverage.wig.txt \
--vcf ${MuTect_dir}${Blood}
${Nevus}.vcf \
--analysis_type MuTect --reference_sequence ${GATK_hg} --cosmic ${COSMIC} --dbsnp ${dbSNP} --intervals ${Intervals} \
--disable_auto_index_creation_and_locking_when_reading_rods \
--min_qscore 30 --max_alt_alleles_in_normal_count 0

Only the last line is added in the stringent running.

To my surprise, I got about 30 more mutations on the second running. Total 9 pairs of samples. It this possible?
This probably possible for small number of mutations, but we are doing melanoma, with large number of mutations (over 2000 from 9 patient). Can this still happen? Or does this indicate any mistake I made?

Tagged:

Issue · Github
by Sheila

Issue Number
1029
State
closed
Last Updated
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Milestone
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vdauwera

Answers

  • Haiying7Haiying7 Heidelberg, GermanyMember

    In both run, I used MuTect-1.1.7.
    The data is whole exome sequence data from matched tomor and normal samples.
    Please let me know if I need to provide more information.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We're following up on this in your other thread. Next time, please don't repost. If there's a lag before we answer it means we're busy, not that we're not paying attention to the forum.

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