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Hello,
I am trying to find out Somatic mutations Using VarScan in RNA seq Data.
Can Varscan detect them in RNA seq ?
1. Has anyone used it previously on RNA ?
2. I used the following steps:
- samtools sort .bam
- samtools mpileup -B -q 1 -f ref.fa tumor.sorted.bam > tumor.sorted.pileup
- java -jar varscan somatic control.sorted.pileup tumor.sorted.pileup --output-snp somatic_output.snp --output-indel somatic_output.indel
The commands are still running.
I looked at the .snp and .indel files.
The output files look this way
chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
chr1 20121 N A 0 8 100% A 0 8 100% A Germline 1.6636709775210046E-9 1.0 0 0 0 8
chr1 20122 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20123 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20124 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20125 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20126 N C 0 9 100% C 0 8 100% C Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20127 N C 0 8 100% C 0 8 100% C Germline 1.6636709775210046E-9 1.0 0 0 0 8
chr1 20128 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20129 N C/NC 0 7 100% C 0 5 100% NC Unknown 1.0 1.0 0 0 0 5
chr1 20130 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20131 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20132 N T 0 9 100% T 0 8 100% T Germline 4.2852131239177147E-10 1.0 0 0 0 8
There are some places which show unknown and I dont find Somatic in anywhere.
Whats the reason ?
Are any of the above steps wrong ?
Can anyone help me with this ?
Thanks !
I am trying to find out Somatic mutations Using VarScan in RNA seq Data.
Can Varscan detect them in RNA seq ?
1. Has anyone used it previously on RNA ?
2. I used the following steps:
- samtools sort .bam
- samtools mpileup -B -q 1 -f ref.fa tumor.sorted.bam > tumor.sorted.pileup
- java -jar varscan somatic control.sorted.pileup tumor.sorted.pileup --output-snp somatic_output.snp --output-indel somatic_output.indel
The commands are still running.
I looked at the .snp and .indel files.
The output files look this way
chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
chr1 20121 N A 0 8 100% A 0 8 100% A Germline 1.6636709775210046E-9 1.0 0 0 0 8
chr1 20122 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20123 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20124 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20125 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20126 N C 0 9 100% C 0 8 100% C Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20127 N C 0 8 100% C 0 8 100% C Germline 1.6636709775210046E-9 1.0 0 0 0 8
chr1 20128 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20129 N C/NC 0 7 100% C 0 5 100% NC Unknown 1.0 1.0 0 0 0 5
chr1 20130 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20131 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
chr1 20132 N T 0 9 100% T 0 8 100% T Germline 4.2852131239177147E-10 1.0 0 0 0 8
There are some places which show unknown and I dont find Somatic in anywhere.
Whats the reason ?
Are any of the above steps wrong ?
Can anyone help me with this ?
Thanks !
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